HUMAN HEALTH AND

DISEASE
BIOLOGY INVESTIGATORY PROJECT:-

PREPARED BY
MASTER ADITYA SWARNAKAR
ROLL NO. .., CLASS-XII
KENDRIYA VIDYALAYA, SECTOR-6,
ROURKELA

GUIDED BY Ms, SANDHYA KHALKO,

LABORATORY CERTIFICATE
Certified that this is the bonafide record of the work done by Master
AdityaSwarnakar bearing Roll No of class XII in the academic
session 2015-16 in the Biology laboratory of Kendriya Vidyalaya, Sector6, Rourkela.
The Project has been done in the intellectual and inspiring
environment of Ms.Sandhya Khalko.

Signature of Student

Signature of External

Signature of Internal

ACKNOWLEDGEMENT

I am thankful to Kendriya Vidyalaya, Sector-6, Rourkela for giving me an

opportunity to prove my skills. In the process of preparing the project I have made use
of theoretical knowledge that I have gained in my class.
I owe my sincere thanks to my Biology teacher Ms.Sandhya Khalko without
whose intervention this project would not have been the same. Her constant motivation
and positive complement have added to the successive completion of the project.
Lastly, I express my sincere thanks to my family and friends who have extended
helping hands in completing the project.

Signature of Student

Signature of Teacher

Signature of External

KENDRIYA VIDYALAYA
SECTOR-6, ROURKELA
PHYSICS INVESTIGATORY PROJECT
2015-16
AIM TO DETERMINE THE REFRACTIVE INDEX OF VARIOUS LIQUID USING
RECTAGULAR HOLLOW GLASS SLAB.

LABORATRY CERTIFICATE
This is to certify that Aditya Swarnakar a student of class XII has successfully
completed the research project on the topic to determine the refractive index of various
liquid using rectangular hollow glass slab under the guidance of Mr. L. M. Sahu (subject
teacher).

The references taken in making this project have been declared at the end of the report.

Signature of Examiner

Signature of lab in charge

Signature of Principal

DECLARATION
I Aditya Swarnakar of class XII has successfully completed the research project
on the topic to determine the refractive index of various liquid using rectangular hollow
glass slab is done by me under the guidance of our teacher Mr. L. M. Sahu.
Name- Aditya Swarnakar
Class-XII
Roll No.-

ACKNOWLEDGEMENT
I wish my gratitude and sincere thanks to our principal for his encouragement
and for all the facilities that he provided for this project work. I sincerely appreciate his
magnanimity by taking of into his folds for which I shall remain indebted to him. I extend
my hereby thanks to Mr. L. M. Sahu our Physics teacher, who guided me to the
successful completion of this project.
I cannot forge to offer my sincere thanks to my friends who helped me to carry
out the project successfully and for the valuable advice and support, which I received
from them time to time.
Name- Aditya Swarnakar
Class-XII
Roll No.-

Biomolecule
From Wikipedia, the free encyclopedia

A representation of the 3D structure of myoglobin, showingalpha helices, represented by ribbons. This protein
was the first to have its structure solved by X-ray crystallography by Max Perutz andSir John Cowdery
Kendrew in 1958, for which they received a Nobel Prize in Chemistry

A biomolecule is any molecule that is present in living organisms, including

largemacromolecules such as proteins, carbohydrates, lipids, and nucleic acids, as well assmall
molecules such as primary metabolites, secondary metabolites, and natural products. A more
general name for this class of material is biological materials. Biomolecules are
usually endogenous but may also be exogenous. For example,pharmaceutical drugs may be natural
products or semisynthetic (biopharmaceuticals) or they may be totally synthetic.
Contents

Biomolecular engineering is the application of engineering principles and practices to

the purposeful manipulation of molecules of biological origin. Biomolecular engineers integrate
knowledge of biological processes with the core knowledge of chemical engineering in order to focus
on molecular level solutions to issues and problems in the life sciences related to
the environment, agriculture, energy, industry, food production, biotechnology and medicine.
Biomolecular engineers purposefully manipulate carbohydrates, proteins, nucleic
acids and lipids within the framework of the relation between their structure (see: nucleic acid
structure, carbohydrate chemistry, protein structure,), function (see: protein function) and properties
and in relation to applicability to such areas as environmental remediation, crop and live stock
production, biofuel cells and biomolecular diagnostics. Fundamental attention is given to the
thermodynamics and kinetics of molecular recognition in enzymes, antibodies, DNA
hybridization, bio-conjugation/bio-immobilization and bioseparations. Attention is also given to the
rudiments of engineered biomolecules in cell signaling, cell growth kinetics, biochemical pathway
engineering and bioreactor engineering. Biomolecular engineers are leading the major shift towards
understanding and controlling the molecular mechanisms that define life as we know it.
Contents
[hide]

1Timeline
o

1.1History

1.2Future

2Basic biomolecules

2.1Proteins

2.2Carbohydrates

2.3Nucleic acids

2.4Lipids

3Biomolecular engineering of molecules

o

3.1Recombinant DNA

3.1.1Method

3.1.2Applications

3.2Site-directed mutagenesis

3.2.1General procedure

3.2.2Applications

3.3Bio-immobilization and bio-conjugation

3.4Polymerase chain reaction

3.5Enzyme-linked immunosorbent assay (ELISA)

3.4.1Biomolecular engineering techniques involved in PCR

3.5.1Biomolecular engineering techniques involved in ELISA

4Applications and fields

o

4.1Biomolecular engineering in industry

4.1.1Scale-up

4.2Related industries

4.2.1Bioengineering

4.2.2Biochemistry

4.2.3Biochemical engineering

4.2.4Biotechnology

4.2.5Bioelectrical engineering

4.2.6Biomedical engineering

4.3Chemical engineering

4.4Education and programs

5See also

6References

7Further reading

8External links

Timeline[edit]
History[edit]
During World War II,[1] the need for large quantities of penicillin of acceptable quality brought together
chemical engineers and microbiologists to focus on penicillin production. This created the right
conditions to start a chain of reactions that lead to the creation of the field of biomolecular
engineering. Biomolecular engineering was first defined in 1992 by the National Institutes of
Health as research at the interface of chemical engineering and biology with an emphasis at the
molecular level". Although first defined as research, biomolecular engineering has since become an
academic discipline and a field of engineering practice. Herceptin, a humanized Mab for breast
cancer treatment, became the first drug designed by a biomolecular engineering approach and was
approved by the FDA. Also, Biomolecular Engineering was a former name of the journal New
Biotechnology.

Future[edit]
Bio-inspired technologies of the future can help explain biomolecular engineering. Looking at
the Moore's law "Prediction", in the future quantum and biology-based processors are "big"
technologies. With the use of biomolecular engineering, the way our processors work can be
manipulated in order to function in the same sense a biological cell work. Biomolecular engineering
has the potential to become one of the most important scientific disciplines because of its
advancements in the analyses of gene expression patterns as well as the purposeful manipulation of
many important biomolecules to improve functionality. Research in this field may lead to new drug
discoveries, improved therapies, and advancement in new bioprocess technology. With the
increasing knowledge of biomolecules, the rate of finding new high-value molecules including but not
limited to antibodies, enzymes, vaccines, and therapeutic peptides will continue to accelerate.
Biomolecular engineering will produce new designs for therapeutic drugs and high-value
biomolecules for treatment or prevention of cancers, genetic diseases, and other types of metabolic
diseases. Also, there is anticipation of industrial enzymes that are engineered to have desirable
properties for process improvement as well the manufacturing of high-value biomolecular products at
a much lower production cost. Using recombinant technology, new antibiotics that are active against
resistant strains will also be produced.[2]

Basic biomolecules[edit]
Biomolecular engineering deals with the manipulation of many key biomolecules. These include, but
are not limited to, proteins, carbohydrates, nucleic acids, and lipids. These molecules are the basic

building blocks of life and by controlling, creating, and manipulating their form and function there are
many new avenues and advantages available to society. Since every biomolecule is different, there
are a number of techniques used to manipulate each one respectively.

Proteins[edit]
Proteins are polymers that are made up of amino acid chains linked with peptide bonds. They have
four distinct levels of structure: primary, secondary, tertiary, and quaternary. Primary structure refers
to the amino acid backbone sequence. Secondary structure focuses on minor conformations that
develop as a result of the hydrogen bonding between the amino acid chain. If most of the protein
contains intermolecular hydrogen bonds it is said to be fibrillar, and the majority of its secondary
structure will be beta sheets. However, if the majority of the orientation contains intramolecular
hydrogen bonds, then the protein is referred to as globular and mostly consists of alpha helixes.
There are also conformations that consist of a mix of alpha helices and beta sheets as well as a beta
helixes with an alpha sheets.
The tertiary structure of proteins deal with their folding process and how the overall molecule is
arranged. Finally, a quaternary structure is a group of tertiary proteins coming together and binding.
With all of these levels, proteins have a wide variety of places in which they can be manipulated and
adjusted. Techniques are used to affect the amino acid sequence of the protein (site directed
mutagenesis), the folding and conformation of the protein, or the folding of a single tertiary protein
within a quaternary protein matrix. Proteins that are the main focus of manipulation are
typically enzymes. These are proteins that act as catalysts for biochemical reactions. By
manipulating these catalysts, the reaction rates, products, and effects can be controlled. Enzymes
and proteins are important to the biological field and research that there are specific subsets of
engineering focusing only on proteins and enzymes. See protein engineering.

Carbohydrates[edit]
Carbohydrates are another important biomolecule. These are polymers, called polysaccharides,
which are made up of chains of simple sugars connected via glycosidic bonds.
These monosaccharides consist of a five to six carbon ring that contains carbon, hydrogen, and
oxygen - typically in a 1:2:1 ratio, respectively. Common monosaccharides are glucose,fructose, and
ribose. When linked together monosaccharides can form disaccharides, oligosaccharides, and
polysaccharides: the nomenclature is dependent on the number of monosaccharides linked together.
Common dissacharides, two monosaccharides joined together, are sucrose, maltose, and lactose.
Important polysaccharides, links of many monosaccharides, are cellulose, starch, and chitin.
Cellulose is a polysaccharide made up of beta 1-4 linkages between repeat glucose monomers. It is
the most abundant source of sugar in nature and is a major part of the paper industry. Starch is also
a polysaccharide made up of glucose monomers; however, they are connected via an alpha 1-4
linkage instead of beta. Starches, particularly amylase, are important in many industries, including
the paper, cosmetic, and food. Chitin is a derivation of cellulose, possessing anacetamide group
instead of an OH on one of its carbons. Acetimide group is deacetylated the polymer chain is then
calledchitosan. Both of these cellulose derivatives are a major source of research for the biomedical
and food industries. They have been shown to assist with blood clotting, have antimicrobial
properties, and dietary applications. A lot of engineering and research is focusing on the degree
of deacetylation that provides the most effective result for specific applications.

Nucleic acids[edit]
Nucleic acids are macromolecules that consist of DNA and RNA which are biopolymers consisting of
chains of biomolecules. These two molecules are the genetic code and template that make life
possible. Manipulation of these molecules and structures causes major changes in function and
expression of other macromolecules. Nucleosides are glycosylamines containing a nucleobase
bound to either ribose or deoxyribose sugar via a beta-glycosidic linkage. The sequence of the

bases determine the genetic code. Nucleotides are nucleosides that are phosphorylated by
specific kinases via aphosphodiester bond.[3] Nucleotides are the repeating structural units of nucleic
acids. The nucleotides are made of a nitrogenous base, a pentose (ribose for RNA or deoxyribose
for DNA), and three phosphate groups. See, Site-directed mutagenesis, recombinant DNA,
and ELISAs.

Lipids[edit]
Lipids are biomolecules that are made up of glycerol derivatives bonded with fatty
acid chains. Glycerol is a simple polyolthat has a formula of C3H5(OH)3. Fatty acids are long carbon
chains that have a carboxylic acid group at the end. Thecarbon chains can be either saturated with
hydrogen; every carbon bond is occupied by a hydrogen atom or a single bond to another carbon in
the carbon chain, or they can be unsaturated; namely, there are double bonds between the carbon
atoms in the chain. Common fatty acids include lauric acid, stearic acid, and oleic acid. The study
and engineering of lipids typically focuses on the manipulation of lipid membranes and
encapsulation. Cellular membranes and other biological membranes typically consist of
a phospholipid bilayer membrane, or a derivative thereof. Along with the study of cellular
membranes, lipids are also important molecules for energy storage. By utilizing encapsulation
properties and thermodynamiccharacteristics, lipids become significant assets in structure
and energy control when engineering molecules.

Biomolecular engineering of molecules[edit]

Recombinant DNA[edit]
Main article: Recombinant DNA
Recombinant DNA are DNA biomolecules that contain genetic sequences that are not native to the
organisms genome. Using recombinant techniques, it is possible to insert, delete, or alter a DNA
sequence precisely without depending on the location of restriction sites. There are a wide range of
applications for which recombinant DNA is used.
Method[edit]

Creating recombinant DNA. After the plasmid is cleaved by restriction enzymes, ligases insert the foreign DNA
fragments into the plasmid.

The traditional method for creating recombinant DNA typically involves the use ofplasmids in the
host bacteria. The plasmid contains a genetic sequence corresponding to the recognition site of a
restriction endonuclease, such as EcoR1. After foreign DNA fragments, which have also been cut
with the same restriction endonuclease, have been inserted into host cell, the restriction
endonuclease gene is expressed by applying heat,[4] or by introducing a biomolecule, such as
arabinose.[5] Upon expression, the enzyme will cleave the plasmid at its corresponding recognition
site creating sticky ends on the plasmid. Ligases then joins the sticky ends to the corresponding
sticky ends of the foreign DNA fragments creating a recombinant DNA plasmid.

Advances in genetic engineering have made the modification of genes in microbes quite efficient
allowing constructs to be made in about a weeks worth of time. It has also made it possible to modify
the organism's genome itself. Specifically, use of the genes from the bacteriophage lambda are used
in recombination.[6] This mechanism, known as recombineering, utilizes the three proteins Exo, Beta,
and Gam, which are created by the genes exo, bet, and gam respectively. Exo is a double stranded
DNA exonuclease with 5 to 3 activity. It cuts the double stranded DNA leaving 3 overhangs. Beta is
a protein that binds to single stranded DNA and assists homologous recombination by promoting
annealing between the homology regions of the inserted DNA and the chromosomal DNA. Gam
functions to protect the DNA insert from being destroyed by nativenucleases within the cell.
Applications[edit]
Recombinant DNA can be engineered for a wide variety of purposes. The techniques utilized allow
for specific modification of genes making it possible to modify any biomolecule. It can be engineered
for laboratory purposes, where it can be used to analyze genes in a given organism. In the
pharmaceutical industry, proteins can be modified using recombination techniques. Some of these
proteins include human insulin. Recombinant insulin is synthesized by inserting the human insulin
gene into E. coli, which then produces insulin for human use.[7][8] Other proteins, such as human
growth hormone,[9] factor VIII, and hepatitis B vaccine are produced using similar means.
Recombinant DNA can also be used for diagnostic methods involving the use of the ELISA method.
This makes it possible to engineer antigens, as well as the enzymes attached, to recognize different
substrates or be modified for bioimmobilization. Recombinant DNA is also responsible for many
products found in the agricultural industry. Genetically modified food, such as golden rice,[10] has
been engineered to have increased production of vitamin A for use in societies and cultures where
dietary vitamin A is scarce. Other properties that have been engineered into crops include herbicideresistance[11] and insect-resistance.[12]

Site-directed mutagenesis[edit]
Site-directed mutagenesis is a technique that has been around since the 1970s. The early days of
research in this field yielded discoveries about the potential of certain chemicals such as bisulfite
and aminopurine to change certain bases in a gene. This research continued, and other processes
were developed to create certain nucleotide sequences on a gene, such as the use of restriction
enzymes to fragment certain viral strands and use them as primers for bacterial plasmids. The
modern method, developed by Michael Smith in 1978, uses an oligonucleotide that is
complementary to a bacterial plasmid with a single base pair mismatch or a series of mismatches. [13]
General procedure[edit]
Site directed mutagenesis is a valuable technique that allows for the replacement of a single base in
an oligonucleotide or gene. The basics of this technique involve the preparation of a primer that will
be a complementary strand to a wild type bacterial plasmid. This primer will have a base pair
mismatch at the site where the replacement is desired. The primer must also be long enough such
that the primer will anneal to the wild type plasmid. After the primer anneals, a DNA polymerase will
complete the primer. When the bacterial plasmid is replicated, the mutated strand will be replicated
as well. The same technique can be used to create a gene insertion or deletion. Often, an antibiotic
resistant gene is inserted along with the modification of interest and the bacteria are cultured on an
antibiotic medium. The bacteria that were not successfully mutated will not survive on this medium,
and the mutated bacteria can easily be cultured.

This animation shows the basic steps of site directed mutagenesis, where X-Y is the desired base pair
replacement of T-A.

Applications[edit]
Site-directed mutagenesis can be useful for many different reasons. A single base pair replacement,
could change a codon, and thus replace an amino acid in a protein. This is useful for studying the
way certain proteins behave. It is also useful because enzymes can be purposefully manipulated by
changing certain amino acids. If an amino acid is changed that is in close proximity to the active site,
the kinetic parameters may change drastically, or the enzyme might behave in a different way.
Another application of site directed mutagenesis is exchanging an amino acid residue far from the
active site with a lysine residue or cysteine residue. These amino acids make it easier to covalently
bond the enzyme to a solid surface, which allows for enzyme re-use and use of enzymes in
continuous processes. Sometimes, amino acids with non-natural functional groups (such as ketones
and azides) are added to proteins[14] These additions may be for ease of bioconjugation, or to study
the effects of amino acid changes on the form and function of the proteins. The coupling of site
directed mutagenesis and PCR are being utilized to reduce interleukin-6 activity in cancerous cells.
[15]
The bacteria bacillus subtilis is often used in site directed mutagenesis.[16] The bacteria secretes an
enzyme called subtilisin through the cell wall. Biomolecular engineers can purposely manipulate this
gene to essentially make the cell a factory for producing whatever protein the insertion in the gene
codes.

Bio-immobilization and bio-conjugation[edit]

Bio-immobilization and bio-conjugation is the purposeful manipulation of a biomolecules mobility by
chemical or physical means to obtain a desired property. Immobilization of biomolecules allows
exploiting characteristics of the molecule under controlled environments. For example [17] , the
immobilization of glucose oxidase on calcium alginate gel beads can be used in a bioreactor. The
resulting product will not need purification to remove the enzyme because it will remain linked to the
beads in the column. Examples of types of biomolecules that are immobilized are enzymes,
organelles, and complete cells. Biomolecules can be immobilized using a range of techniques. The
most popular are physical entrapment, adsorption, and covalent modification.

Physical entrapment[18] - the use of a polymer to contain the

biomolecule in a matrix without chemical modification. Entrapment
can be between lattices of polymer, known as gel entrapment, or
within micro-cavities of synthetic fibers, known as fiber entrapment.
Examples include entrapment of enzymes such as glucose oxidase
in gel column for use as abioreactor. Important characteristic with
entrapment is biocatalyst remains structurally unchanged, but
creates large diffusion barriers for substrates.

Adsorption- immobilization of biomolecules due to interaction

between the biomolecule and groups on support. Can be physical
adsorption, ionic bonding, or metal binding chelation. Such
techniques can be performed under mild conditions and relatively
simple, although the linkages are highly dependent upon pH,
solvent and temperature. Examples include enzyme-linked
immunosorbent assays.

Covalent modification- involves chemical reactions between certain

functional groups and matrix. This method forms stable complex
between biomolecule and matrix and is suited for mass production.
Due to the formation of chemical bond to functional groups, loss of
activity can occur. Examples of chemistries used are DCC
coupling[19] PDC coupling and EDC/NHS coupling, all of which take
advantage of the reactive amines on the biomolecules surface.

Because immobilization restricts the biomolecule, care must be given to ensure that functionality is
not entirely lost. Variables to consider are pH,[20] temperature, solvent choice, ionic strength,
orientation of active sites due to conjugation. For enzymes, the conjugation will lower the kinetic rate
due to a change in the 3-dimensional structure, so care must be taken to ensure functionality is not
lost. Bio-immobilization is used in technologies such as diagnostic bioassays, biosensors,ELISA,
and bioseparations. Interleukin (IL-6) can also be bioimmobilized on biosensors. The ability to
observe these changes in IL-6 levels is important in diagnosing an illness. A cancer patient will have
elevated IL-6 level and monitoring those levels will allow the physician to watch the disease
progress. A direct immobilization of IL-6 on the surface of a biosensor offers a fast alternative
to ELISA.[21]

Polymerase chain reaction[edit]

Main article: Polymerase chain reaction

Polymerase chain reaction. There are three main steps involved in PCR. In the first step, the double stranded
DNA strands are "melted" or denatured forming single stranded DNA. Next, primers, which have been designed
to target a specific gene sequence on the DNA, anneal to the single stranded DNA. Lastly, DNA polymerase
synthesizes a new DNA strand complimentary to the original DNA. These three steps are repeated multiple
times until the desired number of copies are made.

The polymerase chain reaction (PCR) is a scientific technique that is used to replicate a piece of
a DNA molecule by several orders of magnitude. PCR implements a cycle of repeated heated and
cooling known as thermal cycling along with the addition of DNA primers and DNA polymerases to
selectively replicate the DNA fragment of interest. The technique was developed by Kary Mullis in
1983 while working for the Cetus Corporation.Mullis would go on to win the Nobel Prize in
Chemistry in 1993 as a result of the impact thatPCR had in many areas such as DNA cloning, DNA
sequencing, and gene analysis.[22]
Biomolecular engineering techniques involved in PCR[edit]
A number of biomolecular engineering strategies have played a very important role in the
development and practice of PCR. For instance a crucial step in insuring the accurate replication of
the desired DNA fragment is the creation of the correct DNA primer. The most common method of
primer synthesis is by the phosphoramidite method. This method includes the biomolecular
engineering of a number of molecules to attain the desired primer sequence. The most prominent
biomolecular engineering technique seen in this primerdesign method is the initial bioimmobilization
of a nucleotide to a solid support. This step is commonly done via the formation of a covalent bond
between the 3-hydroxy group of the first nucleotide of the primer and the solid support material. [23]
Furthermore, as the DNA primer is created certain functional groups of nucleotides to be added to
the growing primer require blocking to prevent undesired side reactions. This blocking of functional
groups as well as the subsequent de-blocking of the groups, coupling of subsequent nucleotides,
and eventual cleaving from the solid support[23] are all methods of manipulation of biomolecules that
can be attributed to biomolecular engineering. The increase in interleukin levels is directly
proportional to the increased death rate in breast cancer patients. PCR paired with Western blotting
and ELISA help define the relationship between cancer cells and IL-6. [24]

Enzyme-linked immunosorbent assay (ELISA) [edit]

Main article: ELISA
Enzyme-linked immunosorbent assay is an assay that utilizes the principle of antibodyantigen recognition to test for the presence of certain substances. The three main types
ofELISA tests which are indirect ELISA, sandwich ELISA, and competitive ELISA all rely on the fact
that antibodies have an affinity for only one specific antigen. Furthermore,
theseantigens or antibodies can be attached to enzymes which can react to create a colorimetric
result indicating the presence of the antibody or antigen of interest.[25] Enzyme linked immunosorbent
assays are used most commonly as diagnostic tests to detect HIV antibodies in blood samples to
test for HIV, human chorionic gonadotropin molecules in urine to indicate pregnancy,
and Mycobacterium tuberculosis antibodies in blood to test patients for tuberculosis.
Furthermore, ELISA is also widely used as a toxicology screen to test people's serum for the
presence of illegal drugs.
Biomolecular engineering techniques involved in ELISA[edit]
Although there are three different types of solid state enzyme-linked immunosorbent assays, all
three types begin with the bioimmobilization of either an antibody or antigen to a surface. This
bioimmobilization is the first instance of biomolecular engineering that can be seen
in ELISA implementation. This step can be performed in a number of ways including a covalent

linkage to a surface which may be coated with protein or another substance. The bioimmobilization
can also be performed via hydrophobic interactions between the molecule and the surface. Because
there are many different types of ELISAs used for many different purposes the biomolecular
engineering that this step requires varies depending on the specific purpose of the ELISA.
Another biomolecular engineering technique that is used in ELISA development is
the bioconjugation of an enzyme to either an antibody or antigen depending on the type of ELISA.
There is much to consider in this enzyme bioconjugation such as avoiding interference with
the active site of the enzyme as well as the antibody binding site in the case that the antibody is
conjugated with enzyme. This bioconjugation is commonly performed by creating crosslinks between
the two molecules of interest and can require a wide variety of different reagents depending on the
nature of the specific molecules.[26]
Interleukin (IL-6) is a signaling protein that has been known to be present during an immune
response. The use of the sandwich type ELISA quantifies the presence of this cytokine within spinal
fluid or bone marrow samples.[27]

Applications and fields[edit]

Biomolecular engineering in industry[edit]

Graph showing number of biotech companies per country[28]

Graph showing percentages of biotech firms by application [29]

Biomolecular engineering is an extensive discipline with applications in many different industries and
fields. As such, it is difficult to pinpoint a general perspective on the Biomolecular engineering
profession. The biotechnology industry, however, provides an adequate representation. The
biotechnology industry, or biotech industry, encompasses all firms that use biotechnology to produce
goods or services or to perform biotechnology research and development. [28] In this way, it
encompasses many of the industrial applications of the biomolecular engineering discipline. By
examination of the biotech industry, it can be gathered that the principal leader of the industry is the

United States, followed by France and Spain.[28] It is also true that the focus of the biotechnology
industry and the application of biomolecular engineering is primarily clinical and medical. People are
willing to pay for good health, so most of the money directed towards the biotech industry stays in
health-related ventures.[citation needed]
Scale-up[edit]
Scaling up a process involves using data from an experimental-scale operation (model or pilot plant)
for the design of a large (scaled-up) unit, of commercial size. Scaling up is a crucial part of
commercializing a process. For example, insulinproduced by genetically modified Escherichia
coli bacteria was initialized on a lab-scale, but to be made commercially viable had to be scaled up
to an industrial level. In order to achieve this scale-up a lot of lab data had to be used to design
commercial sized units. For example, one of the steps in insulin production involves the
crystallization of high purity glargin insulin.[30] In order to achieve this process on a large scale we
want to keep the Power/Volume ratio of both the lab-scale and large-scale crystallizers the same in
order to achieve homogeneous mixing.[31] We also assume the lab-scale crystallizer has geometric
similarity to the large-scale crystallizer. Therefore,
P/V Ni3di3
where di= crystallizer impeller diameter
Ni= impeller rotation rate

Related industries[edit]
Bioengineering[edit]
Main article: Biological engineering
A broad term encompassing all engineering applied to the life sciences. This field of study utilizes
the principles of biologyalong with engineering principles to create marketable products.
Some bioengineering applications include:

Biomimetics - The study and development of synthetic systems that

mimic the form and function of natural biologically produced
substances and processes.

Bioprocess engineering - The study and development of process

equipment and optimization that aids in the production of many
products such as food and pharmaceuticals.

Industrial microbiology - The implementation of microorganisms in

the production of industrial products such as food andantibiotics.
Another common application of industrial microbiology is the
treatment of wastewater in chemical plants via utilization of
certain microorganisms.

Biochemistry[edit]
Main article: Biochemistry
Biochemistry is the study of chemical processes in living organisms, including, but not limited to,
living matter. Biochemical processes govern all living organisms and living processes and the field of
biochemistry seeks to understand and manipulate these processes.
Biochemical engineering[edit]
Main article: Biochemical engineering

Biocatalysis Chemical transformations using enzymes.

Bioseparations Separation of biologically active molecules.

Thermodynamics and Kinetics (chemistry) Analysis of reactions

involving cell growth and biochemicals.

Bioreactor design and analysis Design of reactors for performing

biochemical transformations.

Biomaterials Design, synthesis and production of new materials to

support cells and tissues.

Genetic engineering Purposeful manipulation of the genomes of

organisms to produce new phenotypic traits.

Bioelectronics, Biosensor and Biochip Engineered devices and

systems to measure, monitor and control biological processes.

Bioprocess engineering Design and maintenance of cell-based

and enzyme-based processes for the production of fine chemicals
and pharmaceuticals.

Biotechnology[edit]
Main article: Biotechnology

Bioelectrical engineering[edit]
Main article: Bioelectric
Bioelectrical engineering involves the electrical fields generated by living cells or organisms.
Examples include the electric potential developed between muscles or nerves of the body. This
discipline requires knowledge in the fields of electricity andbiology to understand and utilize these
concepts to improve or better current bioprocesses or technology.

Bioelectrochemistry - Chemistry concerned with electron/proton

transport throughout the cell

Bioelectronics - Field of research coupling biology and electronics

Biomedical engineering[edit]
Main article: Biomedical engineering
Biomedical engineering is a sub category of bioengineering that uses many of the same principles
but focuses more on the medical applications of the various engineering developments. Some
applications of biomedical engineering include:

Biomaterials - Design of new materials for implantation in the

human body and analysis of their effect on the body.

Cellular engineering Design of new cells using recombinant

DNA and development of procedures to allow normal cells to
adhere to artificial implanted biomaterials

Tissue engineering Design of new tissues from the basic

biological building blocks to form new tissues

Artificial organs Application of tissue engineering to whole organs

Medical imaging Imaging of tissues using CAT

scan, MRI, ultrasound, x-ray or other technologies

Medical Optics and Lasers Application of lasers to medical

diagnosis and treatment

Rehabilitation engineering Design of devices and systems used to

aid the disabled

Man-machine interfacing - Control of surgical robots and remote

diagnostic and therapeutic systems using eye tracking, voice
recognition and muscle and brain wave controls

Human factors and ergonomics Design of systems to improve

human performance in a wide range of applications

Chemical engineering[edit]
Main article: Chemical engineering
Chemical engineering is the processing of raw materials into chemical products. It involves
preparation of raw materials to produce reactants, the chemical reaction of these reactants under
controlled conditions, the separation of products, the recycle of byproducts, and the disposal of
wastes. Each step involves certain basic building blocks called unit operations, such as extraction,
filtration, and distillation.[32] These unit operations are found in all chemical processes. Biomolecular
engineering is a subset of Chemical Engineering that applies these same principles to the
processing of chemical substances made by living organisms.

Education and programs[edit]

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article by adding citations to reliable sources. Unsourced material may be challenged and
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The discipline of biomolecular engineering has become ever more prevalent with the better
understanding and advancement of current sciences and technologies. In previous years,
biomolecular engineering was not a well-known career path, but the growth in popularity of this
subject has resulted in new programs offered to undergraduate and graduate students. [citation needed]
Newly developed and offered undergraduate programs across the United States, often coupled to
the chemical engineering program, allow students to achieve a B.S. degree. According
to ABET (Accreditation Board for Engineering and Technology), biomolecular engineering curricula
"must provide thorough grounding in the basic sciences including chemistry, physics, and biology,
with some content at an advanced level [and] engineering application of these basic sciences to
design, analysis, and control, of chemical, physical, and/or biological processes." [33] Common
curricula consist of major engineering courses including transport, thermodynamics, separations,
and kinetics, with additions of life sciencescourses including biology and biochemistry, and including
specialized biomolecular courses focusing on cell biology, nano- and biotechnology, biopolymers,
etc.[34]

To further education in biomolecular engineering studies, the option to get an M.S. or Ph.D. is
becoming ever more available in various colleges and universities.[citation needed]

1Types of biomolecules

2Nucleosides and nucleotides

o

2.1DNA and RNA structure

3Saccharides

4Lignin

5Lipids

6Amino acids
o

6.1Protein structure

6.1.1Apoenzymes

6.1.2Isoenzymes

7See also

8References

9External links

Types of biomolecules[edit]
A diverse range of biomolecules exist, including:

Biomonomers

Bio-oligo

Small molecules:

Lipids, fatty acids, glycolipids, sterols, glycerolipids

Vitamins

Hormones, neurotransmitters

Metabolites

Monomers, oligomers and polymers:

! Biopolymers

Polymerizationproces
s

Covalent
bondname
between

monomers

Amino acids

Oligopeptides

Polypeptides, proteins
(hemoglobin...)

Polycondensation

Peptide bond

Monosaccharide
s

Oligosaccharide
s

Polysaccharides
(cellulose...)

Polycondensation

Glycosidic
bond

Isoprene

Terpenes

Polyterpenes: cis-1,4polyisoprene natural

rubber and trans-1,4polyisoprene gutta-percha

Polyaddition

Nucleotides

Oligonucleotide
s

Polynucleotides, nucleic
acids (DNA, RNA)

Phosphodiester
bond

Nucleosides and nucleotides[edit]

Main articles: Nucleosides and Nucleotides
Nucleosides are molecules formed by attaching a nucleobase to a ribose or deoxyribose ring.
Examples of these includecytidine (C), uridine (U), adenosine (A), guanosine (G), thymidine (T)
and inosine (I).
Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides.
Both DNA and RNA are polymers, consisting of long, linear molecules assembled
by polymerase enzymes from repeating structural units, or monomerss, of mononucleotides. DNA
uses the deoxynucleotides C, G, A, and T, while RNA uses the ribonucleotides (which have an extra
hydroxyl(OH) group on the pentose ring) C, G, A, and U. Modified bases are fairly common (such as
with methyl groups on the base ring), as found in ribosomal RNA or transfer RNAs or for
discriminating the new from old strands of DNA after replication. [1]
Each nucleotide is made of an acyclic nitrogenous base, a pentose and one to three phosphate
groups. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of
chemical energy (adenosine triphosphateand guanosine triphosphate), participate
in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and
are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine
dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).[2]

DNA and RNA structure[edit]

Main articles: DNA and RNA structure
DNA structure is dominated by the well-known double helix formed by Watson-Crick base-pairing of
C with G and A with T. This is known as B-form DNA, and is overwhelmingly the most favorable and
common state of DNA; its highly specific and stable base-pairing is the basis of reliable genetic
information storage. DNA can sometimes occur as single strands (often needing to be stabilized by

single-strand binding proteins) or as A-form or Z-form helices, and occasionally in more complex 3D
structures such as the crossover at Holliday junctions during DNA replication.[2]

Stereo 3D image of a group I intron ribozyme (PDB file 1Y0Q); gray lines show base pairs; ribbon arrows show
double-helix regions, blue to red from 5' to 3' end; white ribbon is an RNA product.

RNA, in contrast, forms large and complex 3D tertiary structures reminiscent of proteins, as well as
the loose single strands with locally folded regions that constitutemessenger RNA molecules. Those
RNA structures contain many stretches of A-form double helix, connected into definite 3D
arrangements by single-stranded loops, bulges, and junctions.[3] Examples are tRNA,
ribosomes, ribozymes, andriboswitches. These complex structures are facilitated by the fact that
RNA backbone has less local flexibility than DNA but a large set of distinct conformations, apparently
because of both positive and negative interactions of the extra OH on the ribose. [4]Structured RNA
molecules can do highly specific binding of other molecules and can themselves be recognized
specifically; in addition, they can perform enzymatic catalysis (when they are known as "ribozymes",
as initially discovered by Tom Cech and colleagues.[5]

Saccharides[edit]
Monosaccharides are the simplest form of carbohydrates with only one simple sugar. They
essentially contain analdehyde or ketone group in their structure.[6] The presence of an aldehyde
group in a monosaccharide is indicated by the prefix aldo-. Similarly, a ketone group is denoted by
the prefix keto-.[1] Examples of monosaccharides are the hexosesglucose, fructose,
and galactose and pentoses, ribose, and deoxyribose Consumed fructose and glucose have
different rates of gastric emptying, are differentially absorbed and have different metabolic fates,
providing multiple opportunities for 2 different saccharides to differentially affect food intake. [6] Most
saccharides eventually provide fuel for cellular respiration.
Disaccharides are formed when two monosaccharides, or two single simple sugars, form a bond
with removal of water. They can be hydrolyzed to yield their saccharin building blocks by boiling with
dilute acid or reacting them with appropriate enzymes. [1] Examples of disaccharides
include sucrose, maltose, and lactose.
Polysaccharides are polymerized monosaccharides, or complex carbohydrates. They have multiple
simple sugars. Examples are starch, cellulose, and glycogen. They are generally large and often
have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble,
but their many hydroxy groups become hydrated individually when exposed to water, and some
polysaccharides form thick colloidal dispersions when heated in water.[1] Shorter polysaccharides,
with 3 - 10 monomers, are called oligosaccharides.[7] A fluorescent indicator-displacement molecular
imprinting sensor was developed for discriminating saccharides. It successfully discriminated three
brands of orange juice beverage.[8] The change in fluorescence intensity of the sensing films resulting
is directly related to the saccharide concentration.[9]

Lignin[edit]
Lignin is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl linkages. After
cellulose, lignin is the second most abundant biopolymer and is one of the primary structural
components of most plants. It contains subunits derived from p-coumaryl alcohol, coniferyl alcohol,
and sinapyl alcohol[10] and is unusual among biomolecules in that it isracemic. The lack of optical
activity is due to the polymerization of lignin which occurs via free radical coupling reactions in which
there is no preference for either configuration at a chiral center.

Lipids[edit]
Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building blocks of biological
membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of
a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid
tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms
that are connected by single bonds alone (saturated fatty acids) or by both single and double
bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always
an even number.
For lipids present in biological membranes, the hydrophilic head is from one of three classes:

Glycolipids, whose heads contain an oligosaccharide with 1-15

saccharide residues.

Phospholipids, whose heads contain a positively charged group that

is linked to the tail by a negatively charged phosphate group.

Sterols, whose heads contain a planar steroid ring, for

example, cholesterol.

Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units
synthesized from arachidonic acid. They are also known as fatty acids

Amino acids[edit]
Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term
amino acid is used when referring to those amino acids in which the amino and carboxylate
functionalities are attached to the same carbon, plusproline which is not actually an amino acid).
Modified amino acids are sometimes observed in proteins; this is usually the result of enzymatic
modification after translation(protein synthesis). For example, phosphorylation of serine
by kinases and dephosphorylation by phosphatases is an important control mechanism in the cell
cycle. Only two amino acids other than the standard twenty are known to be incorporated into
proteins during translation, in certain organisms:

Selenocysteine is incorporated into some proteins at a UGA codon,

which is normally a stop codon.

Pyrrolysine is incorporated into some proteins at a UAG codon. For

instance, in some methanogens in enzymes that are used to
produce methane.

Besides those used in protein synthesis, other biologically important amino acids
include carnitine (used in lipid transport within a cell), ornithine, GABA and taurine.

Protein structure[edit]
The particular series of amino acids that form a protein is known as that protein's primary structure.
This sequence is determined by the genetic makeup of the individual. It specifies the order of sidechain groups along the linear polypeptide "backbone".
Proteins have two types of well-classified, frequently occurring elements of local structure defined by
a particular pattern ofhydrogen bonds along the backbone: alpha helix and beta sheet. Their number
and arrangement is called the secondary structure of the protein. Alpha helices are regular spirals
stabilized by hydrogen bonds between the backbone CO group (carbonyl) of one amino acid residue
and the backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino acids per
turn, and the amino acid side chains stick out from the cylinder of the helix. Beta pleated sheets are
formed by backbone hydrogen bonds between individual beta strands each of which is in an
"extended", or fully stretched-out, conformation. The strands may lie parallel or antiparallel to each
other, and the side-chain direction alternates above and below the sheet. Hemoglobin contains only
helices, natural silk is formed of beta pleated sheets, and many enzymes have a pattern of
alternating helices and beta-strands. The secondary-structure elements are connected by "loop" or
"coil" regions of non-repetitive conformation, which are sometimes quite mobile or disordered but
usually adopt a well-defined, stable arrangement.[11]
The overall, compact, 3D structure of a protein is termed its tertiary structure or its "fold". It is formed
as result of various attractive forces like hydrogen bonding, disulfide bridges, hydrophobic
interactions, hydrophilic interactions, van der Waals force etc.
When two or more polypeptide chains (either of identical or of different sequence) cluster to form a
protein, quaternary structure of protein is formed. Quaternary structure is an attribute
of polymeric (same-sequence chains) or heteromeric(different-sequence chains) proteins
like hemoglobin, which consists of two "alpha" and two "beta" polypeptide chains.
Apoenzymes[edit]
An apoenzyme (or, generally, an apoprotein) is the protein without any small-molecule cofactors,
substrates, or inhibitors bound. It is often important as an inactive storage, transport, or secretory
form of a protein. This is required, for instance, to protect the secretory cell from the activity of that
protein. Apoenzymes becomes active enzymes on addition of a cofactor. Cofactors can be either
inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds, (e.g., flavin and heme).
Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme,
or coenzymes, which are released from the enzyme's active site during the reaction.
Isoenzymes[edit]
Isoenzymes, or isozymes, are multiple forms of an enzyme, with slightly different protein
sequence and closely similar but usually not identical functions. They are either products of
different genes, or else different products of alternative splicing. They may either be produced in
different organs or cell types to perform the same function, or several isoenzymes may be produced
in the same cell type under differential regulation to suit the needs of changing development or
environment. LDH (lactate dehydrogenase) has multiple isozymes, while fetal hemoglobin is an
example of a developmentally regulated isoform of a non-enzymatic protein. The relative levels of
isoenzymes in blood can be used to diagnose problems in the organ of secretion.

Biomolecular engineering
From Wikipedia, the free encyclopedia

Biomolecular engineering is the application of engineering principles and practices to

the purposeful manipulation of molecules of biological origin. Biomolecular engineers integrate
knowledge of biological processes with the core knowledge of chemical engineering in order to focus
on molecular level solutions to issues and problems in the life sciences related to
the environment, agriculture, energy, industry, food production, biotechnology and medicine.
Biomolecular engineers purposefully manipulate carbohydrates, proteins, nucleic
acids and lipids within the framework of the relation between their structure (see: nucleic acid
structure, carbohydrate chemistry, protein structure,), function (see: protein function) and properties
and in relation to applicability to such areas as environmental remediation, crop and live stock
production, biofuel cells and biomolecular diagnostics. Fundamental attention is given to the
thermodynamics and kinetics of molecular recognition in enzymes, antibodies, DNA
hybridization, bio-conjugation/bio-immobilization and bioseparations. Attention is also given to the
rudiments of engineered biomolecules in cell signaling, cell growth kinetics, biochemical pathway
engineering and bioreactor engineering. Biomolecular engineers are leading the major shift towards
understanding and controlling the molecular mechanisms that define life as we know it.
Contents
[hide]

1Timeline
o

1.1History

1.2Future

2Basic biomolecules
o

2.1Proteins

2.2Carbohydrates

2.3Nucleic acids

2.4Lipids

3Biomolecular engineering of molecules

3.1Recombinant DNA

3.1.1Method

3.1.2Applications

3.2Site-directed mutagenesis

3.2.1General procedure

3.2.2Applications

3.3Bio-immobilization and bio-conjugation

3.4Polymerase chain reaction

3.4.1Biomolecular engineering techniques involved in PCR

3.5Enzyme-linked immunosorbent assay (ELISA)

3.5.1Biomolecular engineering techniques involved in ELISA

4Applications and fields

4.1Biomolecular engineering in industry

4.1.1Scale-up

4.2Related industries

4.2.1Bioengineering

4.2.2Biochemistry

4.2.3Biochemical engineering

4.2.4Biotechnology

4.2.5Bioelectrical engineering

4.2.6Biomedical engineering

4.3Chemical engineering

4.4Education and programs

5See also

6References

7Further reading

8External links

Timeline[edit]
History[edit]
During World War II,[1] the need for large quantities of penicillin of acceptable quality brought together
chemical engineers and microbiologists to focus on penicillin production. This created the right
conditions to start a chain of reactions that lead to the creation of the field of biomolecular
engineering. Biomolecular engineering was first defined in 1992 by the National Institutes of
Health as research at the interface of chemical engineering and biology with an emphasis at the
molecular level". Although first defined as research, biomolecular engineering has since become an
academic discipline and a field of engineering practice. Herceptin, a humanized Mab for breast
cancer treatment, became the first drug designed by a biomolecular engineering approach and was
approved by the FDA. Also, Biomolecular Engineering was a former name of the journal New
Biotechnology.

Future[edit]
Bio-inspired technologies of the future can help explain biomolecular engineering. Looking at
the Moore's law "Prediction", in the future quantum and biology-based processors are "big"
technologies. With the use of biomolecular engineering, the way our processors work can be
manipulated in order to function in the same sense a biological cell work. Biomolecular engineering
has the potential to become one of the most important scientific disciplines because of its
advancements in the analyses of gene expression patterns as well as the purposeful manipulation of
many important biomolecules to improve functionality. Research in this field may lead to new drug
discoveries, improved therapies, and advancement in new bioprocess technology. With the
increasing knowledge of biomolecules, the rate of finding new high-value molecules including but not
limited to antibodies, enzymes, vaccines, and therapeutic peptides will continue to accelerate.
Biomolecular engineering will produce new designs for therapeutic drugs and high-value
biomolecules for treatment or prevention of cancers, genetic diseases, and other types of metabolic
diseases. Also, there is anticipation of industrial enzymes that are engineered to have desirable
properties for process improvement as well the manufacturing of high-value biomolecular products at
a much lower production cost. Using recombinant technology, new antibiotics that are active against
resistant strains will also be produced.[2]

Basic biomolecules[edit]
Biomolecular engineering deals with the manipulation of many key biomolecules. These include, but
are not limited to, proteins, carbohydrates, nucleic acids, and lipids. These molecules are the basic
building blocks of life and by controlling, creating, and manipulating their form and function there are
many new avenues and advantages available to society. Since every biomolecule is different, there
are a number of techniques used to manipulate each one respectively.

Proteins[edit]

Proteins are polymers that are made up of amino acid chains linked with peptide bonds. They have
four distinct levels of structure: primary, secondary, tertiary, and quaternary. Primary structure refers
to the amino acid backbone sequence. Secondary structure focuses on minor conformations that
develop as a result of the hydrogen bonding between the amino acid chain. If most of the protein
contains intermolecular hydrogen bonds it is said to be fibrillar, and the majority of its secondary
structure will be beta sheets. However, if the majority of the orientation contains intramolecular
hydrogen bonds, then the protein is referred to as globular and mostly consists of alpha helixes.
There are also conformations that consist of a mix of alpha helices and beta sheets as well as a beta
helixes with an alpha sheets.
The tertiary structure of proteins deal with their folding process and how the overall molecule is
arranged. Finally, a quaternary structure is a group of tertiary proteins coming together and binding.
With all of these levels, proteins have a wide variety of places in which they can be manipulated and
adjusted. Techniques are used to affect the amino acid sequence of the protein (site directed
mutagenesis), the folding and conformation of the protein, or the folding of a single tertiary protein
within a quaternary protein matrix. Proteins that are the main focus of manipulation are
typically enzymes. These are proteins that act as catalysts for biochemical reactions. By
manipulating these catalysts, the reaction rates, products, and effects can be controlled. Enzymes
and proteins are important to the biological field and research that there are specific subsets of
engineering focusing only on proteins and enzymes. See protein engineering.

Carbohydrates[edit]
Carbohydrates are another important biomolecule. These are polymers, called polysaccharides,
which are made up of chains of simple sugars connected via glycosidic bonds.
These monosaccharides consist of a five to six carbon ring that contains carbon, hydrogen, and
oxygen - typically in a 1:2:1 ratio, respectively. Common monosaccharides are glucose,fructose, and
ribose. When linked together monosaccharides can form disaccharides, oligosaccharides, and
polysaccharides: the nomenclature is dependent on the number of monosaccharides linked together.
Common dissacharides, two monosaccharides joined together, are sucrose, maltose, and lactose.
Important polysaccharides, links of many monosaccharides, are cellulose, starch, and chitin.
Cellulose is a polysaccharide made up of beta 1-4 linkages between repeat glucose monomers. It is
the most abundant source of sugar in nature and is a major part of the paper industry. Starch is also
a polysaccharide made up of glucose monomers; however, they are connected via an alpha 1-4
linkage instead of beta. Starches, particularly amylase, are important in many industries, including
the paper, cosmetic, and food. Chitin is a derivation of cellulose, possessing anacetamide group
instead of an OH on one of its carbons. Acetimide group is deacetylated the polymer chain is then
calledchitosan. Both of these cellulose derivatives are a major source of research for the biomedical
and food industries. They have been shown to assist with blood clotting, have antimicrobial
properties, and dietary applications. A lot of engineering and research is focusing on the degree
of deacetylation that provides the most effective result for specific applications.

Nucleic acids[edit]

Nucleic acids are macromolecules that consist of DNA and RNA which are biopolymers consisting of
chains of biomolecules. These two molecules are the genetic code and template that make life
possible. Manipulation of these molecules and structures causes major changes in function and
expression of other macromolecules. Nucleosides are glycosylamines containing a nucleobase
bound to either ribose or deoxyribose sugar via a beta-glycosidic linkage. The sequence of the
bases determine the genetic code. Nucleotides are nucleosides that are phosphorylated by
specific kinases via aphosphodiester bond.[3] Nucleotides are the repeating structural units of nucleic
acids. The nucleotides are made of a nitrogenous base, a pentose (ribose for RNA or deoxyribose
for DNA), and three phosphate groups. See, Site-directed mutagenesis, recombinant DNA,
and ELISAs.

Lipids[edit]
Lipids are biomolecules that are made up of glycerol derivatives bonded with fatty
acid chains. Glycerol is a simple polyolthat has a formula of C3H5(OH)3. Fatty acids are long carbon
chains that have a carboxylic acid group at the end. Thecarbon chains can be either saturated with
hydrogen; every carbon bond is occupied by a hydrogen atom or a single bond to another carbon in
the carbon chain, or they can be unsaturated; namely, there are double bonds between the carbon
atoms in the chain. Common fatty acids include lauric acid, stearic acid, and oleic acid. The study
and engineering of lipids typically focuses on the manipulation of lipid membranes and
encapsulation. Cellular membranes and other biological membranes typically consist of
a phospholipid bilayer membrane, or a derivative thereof. Along with the study of cellular
membranes, lipids are also important molecules for energy storage. By utilizing encapsulation
properties and thermodynamiccharacteristics, lipids become significant assets in structure
and energy control when engineering molecules.

Biomolecular engineering of molecules[edit]

Recombinant DNA[edit]
Main article: Recombinant DNA
Recombinant DNA are DNA biomolecules that contain genetic sequences that are not native to the
organisms genome. Using recombinant techniques, it is possible to insert, delete, or alter a DNA
sequence precisely without depending on the location of restriction sites. There are a wide range of
applications for which recombinant DNA is used.
Method[edit]

Creating recombinant DNA. After the plasmid is cleaved by restriction enzymes, ligases insert the foreign DNA
fragments into the plasmid.

The traditional method for creating recombinant DNA typically involves the use ofplasmids in the
host bacteria. The plasmid contains a genetic sequence corresponding to the recognition site of a
restriction endonuclease, such as EcoR1. After foreign DNA fragments, which have also been cut
with the same restriction endonuclease, have been inserted into host cell, the restriction
endonuclease gene is expressed by applying heat,[4] or by introducing a biomolecule, such as
arabinose.[5] Upon expression, the enzyme will cleave the plasmid at its corresponding recognition
site creating sticky ends on the plasmid. Ligases then joins the sticky ends to the corresponding
sticky ends of the foreign DNA fragments creating a recombinant DNA plasmid.
Advances in genetic engineering have made the modification of genes in microbes quite efficient
allowing constructs to be made in about a weeks worth of time. It has also made it possible to modify
the organism's genome itself. Specifically, use of the genes from the bacteriophage lambda are used
in recombination.[6] This mechanism, known as recombineering, utilizes the three proteins Exo, Beta,
and Gam, which are created by the genes exo, bet, and gam respectively. Exo is a double stranded
DNA exonuclease with 5 to 3 activity. It cuts the double stranded DNA leaving 3 overhangs. Beta is
a protein that binds to single stranded DNA and assists homologous recombination by promoting
annealing between the homology regions of the inserted DNA and the chromosomal DNA. Gam
functions to protect the DNA insert from being destroyed by nativenucleases within the cell.
Applications[edit]
Recombinant DNA can be engineered for a wide variety of purposes. The techniques utilized allow
for specific modification of genes making it possible to modify any biomolecule. It can be engineered
for laboratory purposes, where it can be used to analyze genes in a given organism. In the
pharmaceutical industry, proteins can be modified using recombination techniques. Some of these
proteins include human insulin. Recombinant insulin is synthesized by inserting the human insulin
gene into E. coli, which then produces insulin for human use.[7][8] Other proteins, such as human
growth hormone,[9] factor VIII, and hepatitis B vaccine are produced using similar means.
Recombinant DNA can also be used for diagnostic methods involving the use of the ELISA method.
This makes it possible to engineer antigens, as well as the enzymes attached, to recognize different
substrates or be modified for bioimmobilization. Recombinant DNA is also responsible for many
products found in the agricultural industry. Genetically modified food, such as golden rice,[10] has

been engineered to have increased production of vitamin A for use in societies and cultures where
dietary vitamin A is scarce. Other properties that have been engineered into crops include herbicideresistance[11] and insect-resistance.[12]

Site-directed mutagenesis[edit]
Site-directed mutagenesis is a technique that has been around since the 1970s. The early days of
research in this field yielded discoveries about the potential of certain chemicals such as bisulfite
and aminopurine to change certain bases in a gene. This research continued, and other processes
were developed to create certain nucleotide sequences on a gene, such as the use of restriction
enzymes to fragment certain viral strands and use them as primers for bacterial plasmids. The
modern method, developed by Michael Smith in 1978, uses an oligonucleotide that is
complementary to a bacterial plasmid with a single base pair mismatch or a series of mismatches. [13]
General procedure[edit]
Site directed mutagenesis is a valuable technique that allows for the replacement of a single base in
an oligonucleotide or gene. The basics of this technique involve the preparation of a primer that will
be a complementary strand to a wild type bacterial plasmid. This primer will have a base pair
mismatch at the site where the replacement is desired. The primer must also be long enough such
that the primer will anneal to the wild type plasmid. After the primer anneals, a DNA polymerase will
complete the primer. When the bacterial plasmid is replicated, the mutated strand will be replicated
as well. The same technique can be used to create a gene insertion or deletion. Often, an antibiotic
resistant gene is inserted along with the modification of interest and the bacteria are cultured on an
antibiotic medium. The bacteria that were not successfully mutated will not survive on this medium,
and the mutated bacteria can easily be cultured.

This animation shows the basic steps of site directed mutagenesis, where X-Y is the desired base pair
replacement of T-A.

Applications[edit]
Site-directed mutagenesis can be useful for many different reasons. A single base pair replacement,
could change a codon, and thus replace an amino acid in a protein. This is useful for studying the
way certain proteins behave. It is also useful because enzymes can be purposefully manipulated by

changing certain amino acids. If an amino acid is changed that is in close proximity to the active site,
the kinetic parameters may change drastically, or the enzyme might behave in a different way.
Another application of site directed mutagenesis is exchanging an amino acid residue far from the
active site with a lysine residue or cysteine residue. These amino acids make it easier to covalently
bond the enzyme to a solid surface, which allows for enzyme re-use and use of enzymes in
continuous processes. Sometimes, amino acids with non-natural functional groups (such as ketones
and azides) are added to proteins[14] These additions may be for ease of bioconjugation, or to study
the effects of amino acid changes on the form and function of the proteins. The coupling of site
directed mutagenesis and PCR are being utilized to reduce interleukin-6 activity in cancerous cells.
[15]
The bacteria bacillus subtilis is often used in site directed mutagenesis.[16] The bacteria secretes an
enzyme called subtilisin through the cell wall. Biomolecular engineers can purposely manipulate this
gene to essentially make the cell a factory for producing whatever protein the insertion in the gene
codes.

Bio-immobilization and bio-conjugation[edit]

Bio-immobilization and bio-conjugation is the purposeful manipulation of a biomolecules mobility by
chemical or physical means to obtain a desired property. Immobilization of biomolecules allows
exploiting characteristics of the molecule under controlled environments. For example [17] , the
immobilization of glucose oxidase on calcium alginate gel beads can be used in a bioreactor. The
resulting product will not need purification to remove the enzyme because it will remain linked to the
beads in the column. Examples of types of biomolecules that are immobilized are enzymes,
organelles, and complete cells. Biomolecules can be immobilized using a range of techniques. The
most popular are physical entrapment, adsorption, and covalent modification.

Physical entrapment[18] - the use of a polymer to contain the biomolecule in a matrix without
chemical modification. Entrapment can be between lattices of polymer, known as gel
entrapment, or within micro-cavities of synthetic fibers, known as fiber entrapment. Examples
include entrapment of enzymes such as glucose oxidase in gel column for use as abioreactor.
Important characteristic with entrapment is biocatalyst remains structurally unchanged, but
creates large diffusion barriers for substrates.

Adsorption- immobilization of biomolecules due to interaction between the biomolecule and

groups on support. Can be physical adsorption, ionic bonding, or metal binding chelation. Such
techniques can be performed under mild conditions and relatively simple, although the linkages
are highly dependent upon pH, solvent and temperature. Examples include enzyme-linked
immunosorbent assays.

Covalent modification- involves chemical reactions between certain functional groups and
matrix. This method forms stable complex between biomolecule and matrix and is suited for
mass production. Due to the formation of chemical bond to functional groups, loss of activity can
occur. Examples of chemistries used are DCC coupling[19] PDC coupling and EDC/NHS coupling,
all of which take advantage of the reactive amines on the biomolecules surface.

Because immobilization restricts the biomolecule, care must be given to ensure that functionality is
not entirely lost. Variables to consider are pH,[20] temperature, solvent choice, ionic strength,
orientation of active sites due to conjugation. For enzymes, the conjugation will lower the kinetic rate
due to a change in the 3-dimensional structure, so care must be taken to ensure functionality is not

lost. Bio-immobilization is used in technologies such as diagnostic bioassays, biosensors,ELISA,

and bioseparations. Interleukin (IL-6) can also be bioimmobilized on biosensors. The ability to
observe these changes in IL-6 levels is important in diagnosing an illness. A cancer patient will have
elevated IL-6 level and monitoring those levels will allow the physician to watch the disease
progress. A direct immobilization of IL-6 on the surface of a biosensor offers a fast alternative
to ELISA.[21]

Polymerase chain reaction[edit]

Main article: Polymerase chain reaction

Polymerase chain reaction. There are three main steps involved in PCR. In the first step, the double stranded
DNA strands are "melted" or denatured forming single stranded DNA. Next, primers, which have been designed
to target a specific gene sequence on the DNA, anneal to the single stranded DNA. Lastly, DNA polymerase
synthesizes a new DNA strand complimentary to the original DNA. These three steps are repeated multiple
times until the desired number of copies are made.

The polymerase chain reaction (PCR) is a scientific technique that is used to replicate a piece of
a DNA molecule by several orders of magnitude. PCR implements a cycle of repeated heated and
cooling known as thermal cycling along with the addition of DNA primers and DNA polymerases to
selectively replicate the DNA fragment of interest. The technique was developed by Kary Mullis in
1983 while working for the Cetus Corporation.Mullis would go on to win the Nobel Prize in
Chemistry in 1993 as a result of the impact thatPCR had in many areas such as DNA cloning, DNA
sequencing, and gene analysis.[22]

Biomolecular engineering techniques involved in PCR[edit]

A number of biomolecular engineering strategies have played a very important role in the
development and practice of PCR. For instance a crucial step in insuring the accurate replication of
the desired DNA fragment is the creation of the correct DNA primer. The most common method of
primer synthesis is by the phosphoramidite method. This method includes the biomolecular
engineering of a number of molecules to attain the desired primer sequence. The most prominent
biomolecular engineering technique seen in this primerdesign method is the initial bioimmobilization
of a nucleotide to a solid support. This step is commonly done via the formation of a covalent bond
between the 3-hydroxy group of the first nucleotide of the primer and the solid support material. [23]
Furthermore, as the DNA primer is created certain functional groups of nucleotides to be added to
the growing primer require blocking to prevent undesired side reactions. This blocking of functional
groups as well as the subsequent de-blocking of the groups, coupling of subsequent nucleotides,
and eventual cleaving from the solid support[23] are all methods of manipulation of biomolecules that
can be attributed to biomolecular engineering. The increase in interleukin levels is directly
proportional to the increased death rate in breast cancer patients. PCR paired with Western blotting
and ELISA help define the relationship between cancer cells and IL-6. [24]

Enzyme-linked immunosorbent assay (ELISA)[edit]

Main article: ELISA
Enzyme-linked immunosorbent assay is an assay that utilizes the principle of antibodyantigen recognition to test for the presence of certain substances. The three main types
ofELISA tests which are indirect ELISA, sandwich ELISA, and competitive ELISA all rely on the fact
that antibodies have an affinity for only one specific antigen. Furthermore,
theseantigens or antibodies can be attached to enzymes which can react to create a colorimetric
result indicating the presence of the antibody or antigen of interest.[25] Enzyme linked immunosorbent
assays are used most commonly as diagnostic tests to detect HIV antibodies in blood samples to
test for HIV, human chorionic gonadotropin molecules in urine to indicate pregnancy,
and Mycobacterium tuberculosis antibodies in blood to test patients for tuberculosis.
Furthermore, ELISA is also widely used as a toxicology screen to test people's serum for the
presence of illegal drugs.
Biomolecular engineering techniques involved in ELISA[edit]
Although there are three different types of solid state enzyme-linked immunosorbent assays, all
three types begin with the bioimmobilization of either an antibody or antigen to a surface. This
bioimmobilization is the first instance of biomolecular engineering that can be seen
in ELISA implementation. This step can be performed in a number of ways including a covalent
linkage to a surface which may be coated with protein or another substance. The bioimmobilization
can also be performed via hydrophobic interactions between the molecule and the surface. Because
there are many different types of ELISAs used for many different purposes the biomolecular
engineering that this step requires varies depending on the specific purpose of the ELISA.

Another biomolecular engineering technique that is used in ELISA development is

the bioconjugation of an enzyme to either an antibody or antigen depending on the type of ELISA.
There is much to consider in this enzyme bioconjugation such as avoiding interference with
the active site of the enzyme as well as the antibody binding site in the case that the antibody is
conjugated with enzyme. This bioconjugation is commonly performed by creating crosslinks between
the two molecules of interest and can require a wide variety of different reagents depending on the
nature of the specific molecules.[26]
Interleukin (IL-6) is a signaling protein that has been known to be present during an immune
response. The use of the sandwich type ELISA quantifies the presence of this cytokine within spinal
fluid or bone marrow samples.[27]

Applications and fields[edit]

Biomolecular engineering in industry[edit]

Graph showing number of biotech companies per country[28]

Graph showing percentages of biotech firms by application [29]

Biomolecular engineering is an extensive discipline with applications in many different industries and
fields. As such, it is difficult to pinpoint a general perspective on the Biomolecular engineering
profession. The biotechnology industry, however, provides an adequate representation. The
biotechnology industry, or biotech industry, encompasses all firms that use biotechnology to produce

goods or services or to perform biotechnology research and development. [28] In this way, it
encompasses many of the industrial applications of the biomolecular engineering discipline. By
examination of the biotech industry, it can be gathered that the principal leader of the industry is the
United States, followed by France and Spain.[28] It is also true that the focus of the biotechnology
industry and the application of biomolecular engineering is primarily clinical and medical. People are
willing to pay for good health, so most of the money directed towards the biotech industry stays in
health-related ventures.[citation needed]
Scale-up[edit]
Scaling up a process involves using data from an experimental-scale operation (model or pilot plant)
for the design of a large (scaled-up) unit, of commercial size. Scaling up is a crucial part of
commercializing a process. For example, insulinproduced by genetically modified Escherichia
coli bacteria was initialized on a lab-scale, but to be made commercially viable had to be scaled up
to an industrial level. In order to achieve this scale-up a lot of lab data had to be used to design
commercial sized units. For example, one of the steps in insulin production involves the
crystallization of high purity glargin insulin.[30] In order to achieve this process on a large scale we
want to keep the Power/Volume ratio of both the lab-scale and large-scale crystallizers the same in
order to achieve homogeneous mixing.[31] We also assume the lab-scale crystallizer has geometric
similarity to the large-scale crystallizer. Therefore,
P/V Ni3di3
where di= crystallizer impeller diameter
Ni= impeller rotation rate

Related industries[edit]
Bioengineering[edit]
Main article: Biological engineering
A broad term encompassing all engineering applied to the life sciences. This field of study utilizes
the principles of biologyalong with engineering principles to create marketable products.
Some bioengineering applications include:

Biomimetics - The study and development of synthetic systems that mimic the form and
function of natural biologically produced substances and processes.

Bioprocess engineering - The study and development of process equipment and optimization
that aids in the production of many products such as food and pharmaceuticals.

Industrial microbiology - The implementation of microorganisms in the production of industrial

products such as food andantibiotics. Another common application of industrial microbiology is
the treatment of wastewater in chemical plants via utilization of certain microorganisms.

Biochemistry[edit]

Main article: Biochemistry

Biochemistry is the study of chemical processes in living organisms, including, but not limited to,
living matter. Biochemical processes govern all living organisms and living processes and the field of
biochemistry seeks to understand and manipulate these processes.
Biochemical engineering[edit]
Main article: Biochemical engineering

Biocatalysis Chemical transformations using enzymes.

Bioseparations Separation of biologically active molecules.

Thermodynamics and Kinetics (chemistry) Analysis of reactions involving cell growth and
biochemicals.

Bioreactor design and analysis Design of reactors for performing biochemical

transformations.

Biotechnology[edit]
Main article: Biotechnology

Biomaterials Design, synthesis and production of new materials to support cells and
tissues.

Genetic engineering Purposeful manipulation of the genomes of organisms to produce new

phenotypic traits.

Bioelectronics, Biosensor and Biochip Engineered devices and systems to measure,

monitor and control biological processes.

Bioprocess engineering Design and maintenance of cell-based and enzyme-based

processes for the production of fine chemicals and pharmaceuticals.

Bioelectrical engineering[edit]
Main article: Bioelectric
Bioelectrical engineering involves the electrical fields generated by living cells or organisms.
Examples include the electric potential developed between muscles or nerves of the body. This
discipline requires knowledge in the fields of electricity andbiology to understand and utilize these
concepts to improve or better current bioprocesses or technology.

Bioelectrochemistry - Chemistry concerned with electron/proton transport throughout the cell

Bioelectronics - Field of research coupling biology and electronics

Biomedical engineering[edit]
Main article: Biomedical engineering
Biomedical engineering is a sub category of bioengineering that uses many of the same principles
but focuses more on the medical applications of the various engineering developments. Some
applications of biomedical engineering include:

Biomaterials - Design of new materials for implantation in the human body and analysis of
their effect on the body.

Cellular engineering Design of new cells using recombinant DNA and development of
procedures to allow normal cells to adhere to artificial implanted biomaterials

Tissue engineering Design of new tissues from the basic biological building blocks to form
new tissues

Artificial organs Application of tissue engineering to whole organs

Medical imaging Imaging of tissues using CAT scan, MRI, ultrasound, x-ray or other
technologies

Medical Optics and Lasers Application of lasers to medical diagnosis and treatment

Rehabilitation engineering Design of devices and systems used to aid the disabled

Man-machine interfacing - Control of surgical robots and remote diagnostic and therapeutic
systems using eye tracking, voice recognition and muscle and brain wave controls

Human factors and ergonomics Design of systems to improve human performance in a

wide range of applications

Chemical engineering[edit]
Main article: Chemical engineering
Chemical engineering is the processing of raw materials into chemical products. It involves
preparation of raw materials to produce reactants, the chemical reaction of these reactants under
controlled conditions, the separation of products, the recycle of byproducts, and the disposal of
wastes. Each step involves certain basic building blocks called unit operations, such as extraction,
filtration, and distillation.[32] These unit operations are found in all chemical processes. Biomolecular
engineering is a subset of Chemical Engineering that applies these same principles to the
processing of chemical substances made by living organisms.

Education and programs[edit]

The discipline of biomolecular engineering has become ever more prevalent with the better
understanding and advancement of current sciences and technologies. In previous years,
biomolecular engineering was not a well-known career path, but the growth in popularity of this
subject has resulted in new programs offered to undergraduate and graduate students. [citation needed]
Newly developed and offered undergraduate programs across the United States, often coupled to
the chemical engineering program, allow students to achieve a B.S. degree. According
to ABET (Accreditation Board for Engineering and Technology), biomolecular engineering curricula
"must provide thorough grounding in the basic sciences including chemistry, physics, and biology,
with some content at an advanced level [and] engineering application of these basic sciences to
design, analysis, and control, of chemical, physical, and/or biological processes." [33] Common
curricula consist of major engineering courses including transport, thermodynamics, separations,
and kinetics, with additions of life sciencescourses including biology and biochemistry, and including
specialized biomolecular courses focusing on cell biology, nano- and biotechnology, biopolymers,
etc.[34]
To further education in biomolecular engineering studies, the option to get an M.S. or Ph.D. is
becoming ever more available in various colleges and universities

List of biomolecules
From Wikipedia, the free encyclopedia

This is a list of articles that describe particular biomolecules or types of biomolecules.

Contents :

A
B
C
D
E
F
G
H
I
J
K
L
M
N
O

P
Q
R
S
T
U
V
W
X
Y
Z
See also

A[edit]
For substances with an A- or - prefix such as -amylase, please see the parent page (in this
case Amylase).

A23187 (Calcimycin, Calcium Ionophore)

Abamectine

Abietic acid

Acetic acid

Acetylcholine

Actin

Actinomycin D

Adenosine

Adenosine diphosphate (ADP)

Adenosine monophosphate (AMP)

Adenosine triphosphate (ATP)

Adenylate cyclase

Adonitol

Adrenaline, epinephrine

Adrenocorticotropic hormone (ACTH)

Aequorin

Aflatoxin

Agar

Alamethicin

Alanine

Albumins

Aldosterone

Aleurone

Alpha-amanitin

Allantoin

Allethrin

-Amanatin, see Alpha-amanitin

Amino acid

Amylase (also see -amylase)

Anabolic steroid

Anethole

Angiotensinogen

Anisomycin

Antidiuretic hormone (ADH)

Arabinose

Arginine

Ascomycin

Ascorbic acid (vitamin C)

Asparagine

Aspartic acid

Asymmetric dimethylarginine

Atrial-natriuretic peptide (ANP)

Auxin

Avidin

Azadirachtin A C35H44O16

B[edit]

Bacteriocin

Beauvericin

Bicuculline

Bilirubin

Biopolymer

Biotin (Vitamin H)

Brefeldin A

Brassinolide

Brucine

C[edit]

Cadaverine

Caffeine

Calciferol (Vitamin D)

Calcitonin

Calmodulin

Calmodulin

Calreticulin

Camphor - (C10H16O)

Cannabinol - (C21H26O2)

Capsaicin

Carbohydrase

Carbohydrate

Carnitine

Carrageenan

Casein

Caspase

Cellulase

Cellulose - (C6H10O5)x

Cerulenin

Cetrimonium bromide (Cetrimide) - C19H42BrN

Chelerythrine

Chromomycin A3

Chaparonin

Chitin

-Chloralose

Chlorophyll

Cholecystokinin (CCK)

Cholesterol

Choline

Chondroitin sulfate

Cinnamaldehyde

Citral

Citric acid

Citrinin

Citronellal

Citronellol

Citrulline

Cobalamin (vitamin B12)

Coenzyme

Coenzyme Q

Colchicine

Collagen

Coniine

Corticosteroid

Corticosterone

Corticotropin-releasing hormone (CRH)

Cortisol

Creatine

Creatine kinase

Crystallin

-Cyclodextrin

Cyclodextrin glycosyltransferase

Cyclopamine

Cyclopiazonic acid

Cysteine

Cystine

Cytidine

Cytochalasin

Cytochalasin E

Cytochrome

Cytochrome C

Cytochrome c oxidase

Cytochrome c peroxidase

Cytokine

Cytosine C4H5N3O

D[edit]

Deoxycholic acid

DON (DeoxyNivalenol)

Deoxyribofuranose

Deoxyribose

Deoxyribose nucleic acid (DNA)

Dextran

Dextrin

DNA

Dopamine

E[edit]

Enzyme

Ephedrine

Epinephrine C9H13NO3

Erucic acid CH3(CH2)7CH=CH(CH2)11COOH

Erythritol

Erythropoietin (EPO)

Estradiol

Eugenol

F[edit]

Fatty acid

Fibrin

Fibronectin

Folic acid (Vitamin M)

Follicle stimulating hormone (FSH)

Formaldehyde

Formic acid

Formnoci

Fructose

Fumonisin B1

G[edit]

Galactose

Gamma globulin

Gamma-aminobutyric acid

Gamma-butyrolactone

Gamma-hydroxybutyrate (GHB)

Gastrin

Gelatin

Geraniol

Globulin

Glucagon

Glucosamine

Glucose C6H12O6

Glucose oxidase

Glutamic acid

Glutamine

Glutathione

Gluten

Glycerin (glycerol)

Glycine

Glycogen

Glycolic acid

Glycoprotein

Gonadotropin-releasing hormone (GnRH)

Granzyme

Green fluorescent protein

Growth hormone

Growth hormone-releasing hormone (GHRH)

GTPase

Guanine

Guanosine

Guanosine triphosphate (+GTP)

H[edit]

[[Haptog

obin]]

Hematoxylin

Heme

Hemerythrin

Hemocyanin

Hemoglobin

Hemoprotein

Heparan sulfate

High density lipoprotein, HDL

Histamine

Histidine

Histone

Histone methyltransferase

HLA antigen

Homocysteine

Hormone

human chorionic gonadotropin (hCG)

Human growth hormone

Hyaluronate

Hyaluronidase

Hydrogen peroxide

5-Hydroxymethylcytosine

Hydroxyproline

5-Hydroxytryptamine

I[edit]

Indigo dye

Indole

Inosine

Inositol

Insulin

Insulin-like growth factor

Integral membrane protein

Integrase

Integrin

Intein

Interferon

Inulin

Ionomycin

Ionone

Isoleucine

Iron-sulfur cluster

J[edit]
This section is empty. You
can help by adding to it. (July
2010)

K[edit]

K252a

K252b

KT5720

KT5823

Keratin

Kinase

L[edit]
For substances with an l- or L- prefix such as L-alanine or DL-alanine, please see the parent page
(in this case alanine).

Lactase

Lactic acid

Lactose

Lanolin

Lauric acid

Leptin

Leptomycin B

Leucine

Lignin

Limonene

Linalool

Linoleic acid

Linolenic acid

Lipase

Lipid

Lipid anchored protein

Lipoamide

Lipoprotein

Low density lipoprotein, LDL

Luteinizing hormone (LH)

Lycopene

Lysine

Lysozyme

M[edit]

Malic acid

Maltose

Melatonin

Membrane protein

Metalloprotein

Metallothionein

Methionine

Mimosine

Mithramycin A

Mitomycin C

Monomer

Morphine

Mycophenolic acid

Myoglobin

Myosin

N[edit]

Natural phenols

Nucleic Acid

O[edit]

Ochratoxin A

Oestrogens

Oligopeptide

Oligomycin

Orcin

Orexin

Ornithine

Oxalic acid

Oxidase

Oxytocin

P[edit]

p53

PABA

Paclitaxel

Palmitic acid

Pantothenic acid (vitamin B5)

parathyroid hormone (PTH)

Paraprotein

Pardaxin

Parthenolide

Patulin

Paxilline

Penicillic acid

Penicillin

Penitrem A

Peptidase

Pepsin

Peptide

Perimycin

Peripheral membrane protein

Perosamine

Phenethylamine

Phenylalanine

Phosphagen

phosphatase

Phospholipid

Phenylalanine

Phytic acid

Plant hormones

Polypeptide

Polyphenols

Polysaccharides

Porphyrin

Prion

Progesterone

Prolactin (PRL)

Proline

Propionic acid

Protamine

Protease

Protein

Proteinoid

Putrescine

Pyrethrin

Pyridoxine or pyridoxamine (Vitamin B6)

Pyrrolysine

Pyruvic acid

Q[edit]

Quinidine

Quinine

Quinone

R[edit]

Radicicol

Raffinose

Renin

Retinene

Retinol (Vitamin A)

Rhodopsin (visual purple)

Riboflavin (vitamin B2)

Ribofuranose, Ribose

Ribozyme

Ricin

RNA - Ribonucleic acid

RuBisCO

S[edit]

Safrole

Salicylaldehyde

Salicylic acid

Salvinorin-A C23H28O8

Saponin

Secretin

Selenocysteine

Selenomethionine

Selenoprotein

Serine

Serine kinase

Serotonin

Skatole

Signal recognition particle

Somatostatin

Sorbic acid

Squalene

Staurosporin

Stearic acid

Sterigmatocystin

Sterol

Strychnine

Sucrose (sugar)

Sugars (in general)

superoxide

T[edit]

T2 Toxin

Tannic acid

Tannin

Tartaric acid

Taurine

Tetrodotoxin

Thaumatin

Topoisomerase

Tyrosine kinase

Taurine

Testosterone

Tetrahydrocannabinol (THC)

Tetrodotoxin

Thapsigargin

Thaumatin

Thiamine (vitamin B1) C12H17ClN4OSHCl

Threonine

Thrombopoietin

Thymidine

Thymine

Triacsin C

Thyroid-stimulating hormone (TSH)

Thyrotropin-releasing hormone (TRH)

Thyroxine (T4)

Tocopherol (Vitamin E)

Topoisomerase

Triiodothyronine (T3)

Transmembrane receptor

Trichostatin A

Trophic hormone

Trypsin

Tryptophan

Tubulin

Tunicamycin

Tyrosine

U[edit]

Ubiquitin

Uracil

Urea

Urease

Uric acid C5H4N4O3

Uridine

V[edit]

Valine

Valinomycin

Vanabins

Vasopressin

Verruculogen

Vitamins (in general)

Vitamin A (retinol)

Vitamin B ()

Vitamin B1 (thiamine)

Vitamin B2 (riboflavin)

Vitamin B3 (niacin or nicotinic acid)

Vitamin B4 (adenine)

Vitamin B5 (pantothenic acid)

Vitamin B6 (pyridoxine or pyridoxamine)

Vitamin B12 (cobalamin)

Vitamin C (ascorbic acid)

Vitamin D (calciferol)

Vitamin E (tocopherol)

Vitamin F

Vitamin H (biotin)

Vitamin K (naphthoquinone)

Vitamin M (folic acid)

W[edit]

Water

Wortmannin

X[edit]

Xylose

Y[edit]
Z[edit]

Zearalenone

List of biomolecules
From Wikipedia, the free encyclopedia

This is a list of articles that describe particular biomolecules or types of biomolecules.

Contents :

A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y

Z
See also

A[edit]
For substances with an A- or - prefix such as -amylase, please see the parent page (in this
case Amylase).

A23187 (Calcimycin, Calcium Ionophore)

Abamectine

Abietic acid

Acetic acid

Acetylcholine

Actin

Actinomycin D

Adenosine

Adenosine diphosphate (ADP)

Adenosine monophosphate (AMP)

Adenosine triphosphate (ATP)

Adenylate cyclase

Adonitol

Adrenaline, epinephrine

Adrenocorticotropic hormone (ACTH)

Aequorin

Aflatoxin

Agar

Alamethicin

Alanine

Albumins

Aldosterone

Aleurone

Alpha-amanitin

Allantoin

Allethrin

-Amanatin, see Alpha-amanitin

Amino acid

Amylase (also see -amylase)

Anabolic steroid

Anethole

Angiotensinogen

Anisomycin

Antidiuretic hormone (ADH)

Arabinose

Arginine

Ascomycin

Ascorbic acid (vitamin C)

Asparagine

Aspartic acid

Asymmetric dimethylarginine

Atrial-natriuretic peptide (ANP)

Auxin

Avidin

Azadirachtin A C35H44O16

B[edit]

Bacteriocin

Beauvericin

Bicuculline

Bilirubin

Biopolymer

Biotin (Vitamin H)

Brefeldin A

Brassinolide

Brucine

C[edit]

Cadaverine

Caffeine

Calciferol (Vitamin D)

Calcitonin

Calmodulin

Calmodulin

Calreticulin

Camphor - (C10H16O)

Cannabinol - (C21H26O2)

Capsaicin

Carbohydrase

Carbohydrate

Carnitine

Carrageenan

Casein

Caspase

Cellulase

Cellulose - (C6H10O5)x

Cerulenin

Cetrimonium bromide (Cetrimide) - C19H42BrN

Chelerythrine

Chromomycin A3

Chaparonin

Chitin

-Chloralose

Chlorophyll

Cholecystokinin (CCK)

Cholesterol

Choline

Chondroitin sulfate

Cinnamaldehyde

Citral

Citric acid

Citrinin

Citronellal

Citronellol

Citrulline

Cobalamin (vitamin B12)

Coenzyme

Coenzyme Q

Colchicine

Collagen

Coniine

Corticosteroid

Corticosterone

Corticotropin-releasing hormone (CRH)

Cortisol

Creatine

Creatine kinase

Crystallin

-Cyclodextrin

Cyclodextrin glycosyltransferase

Cyclopamine

Cyclopiazonic acid

Cysteine

Cystine

Cytidine

Cytochalasin

Cytochalasin E

Cytochrome

Cytochrome C

Cytochrome c oxidase

Cytochrome c peroxidase

Cytokine

Cytosine C4H5N3O

D[edit]

Deoxycholic acid

DON (DeoxyNivalenol)

Deoxyribofuranose

Deoxyribose

Deoxyribose nucleic acid (DNA)

Dextran

Dextrin

DNA

Dopamine

E[edit]

Enzyme

Ephedrine

Epinephrine C9H13NO3

Erucic acid CH3(CH2)7CH=CH(CH2)11COOH

Erythritol

Erythropoietin (EPO)

Estradiol

Eugenol

F[edit]

Fatty acid

Fibrin

Fibronectin

Folic acid (Vitamin M)

Follicle stimulating hormone (FSH)

Formaldehyde

Formic acid

Formnoci

Fructose

Fumonisin B1

G[edit]

Galactose

Gamma globulin

Gamma-aminobutyric acid

Gamma-butyrolactone

Gamma-hydroxybutyrate (GHB)

Gastrin

Gelatin

Geraniol

Globulin

Glucagon

Glucosamine

Glucose C6H12O6

Glucose oxidase

Glutamic acid

Glutamine

Glutathione

Gluten

Glycerin (glycerol)

Glycine

Glycogen

Glycolic acid

Glycoprotein

Gonadotropin-releasing hormone (GnRH)

Granzyme

Green fluorescent protein

Growth hormone

Growth hormone-releasing hormone (GHRH)

GTPase

Guanine

Guanosine

Guanosine triphosphate (+GTP)

H[edit]

[[Haptog

obin]]

Hematoxylin

Heme

Hemerythrin

Hemocyanin

Hemoglobin

Hemoprotein

Heparan sulfate

High density lipoprotein, HDL

Histamine

Histidine

Histone

Histone methyltransferase

HLA antigen

Homocysteine

Hormone

human chorionic gonadotropin (hCG)

Human growth hormone

Hyaluronate

Hyaluronidase

Hydrogen peroxide

5-Hydroxymethylcytosine

Hydroxyproline

5-Hydroxytryptamine

I[edit]

Indigo dye

Indole

Inosine

Inositol

Insulin

Insulin-like growth factor

Integral membrane protein

Integrase

Integrin

Intein

Interferon

Inulin

Ionomycin

Ionone

Isoleucine

Iron-sulfur cluster

J[edit]
This section is empty. You
can help by adding to it. (July
2010)

K[edit]

K252a

K252b

KT5720

KT5823

Keratin

Kinase

L[edit]
For substances with an l- or L- prefix such as L-alanine or DL-alanine, please see the parent page
(in this case alanine).

Lactase

Lactic acid

Lactose

Lanolin

Lauric acid

Leptin

Leptomycin B

Leucine

Lignin

Limonene

Linalool

Linoleic acid

Linolenic acid

Lipase

Lipid

Lipid anchored protein

Lipoamide

Lipoprotein

Low density lipoprotein, LDL

Luteinizing hormone (LH)

Lycopene

Lysine

Lysozyme

M[edit]

Malic acid

Maltose

Melatonin

Membrane protein

Metalloprotein

Metallothionein

Methionine

Mimosine

Mithramycin A

Mitomycin C

Monomer

Morphine

Mycophenolic acid

Myoglobin

Myosin

N[edit]

Natural phenols

Nucleic Acid

O[edit]

Ochratoxin A

Oestrogens

Oligopeptide

Oligomycin

Orcin

Orexin

Ornithine

Oxalic acid

Oxidase

Oxytocin

P[edit]

p53

PABA

Paclitaxel

Palmitic acid

Pantothenic acid (vitamin B5)

parathyroid hormone (PTH)

Paraprotein

Pardaxin

Parthenolide

Patulin

Paxilline

Penicillic acid

Penicillin

Penitrem A

Peptidase

Pepsin

Peptide

Perimycin

Peripheral membrane protein

Perosamine

Phenethylamine

Phenylalanine

Phosphagen

phosphatase

Phospholipid

Phenylalanine

Phytic acid

Plant hormones

Polypeptide

Polyphenols

Polysaccharides

Porphyrin

Prion

Progesterone

Prolactin (PRL)

Proline

Propionic acid

Protamine

Protease

Protein

Proteinoid

Putrescine

Pyrethrin

Pyridoxine or pyridoxamine (Vitamin B6)

Pyrrolysine

Pyruvic acid

Q[edit]

Quinidine

Quinine

Quinone

R[edit]

Radicicol

Raffinose

Renin

Retinene

Retinol (Vitamin A)

Rhodopsin (visual purple)

Riboflavin (vitamin B2)

Ribofuranose, Ribose

Ribozyme

Ricin

RNA - Ribonucleic acid

RuBisCO

S[edit]

Safrole

Salicylaldehyde

Salicylic acid

Salvinorin-A C23H28O8

Saponin

Secretin

Selenocysteine

Selenomethionine

Selenoprotein

Serine

Serine kinase

Serotonin

Skatole

Signal recognition particle

Somatostatin

Sorbic acid

Squalene

Staurosporin

Stearic acid

Sterigmatocystin

Sterol

Strychnine

Sucrose (sugar)

Sugars (in general)

superoxide

T[edit]

T2 Toxin

Tannic acid

Tannin

Tartaric acid

Taurine

Tetrodotoxin

Thaumatin

Topoisomerase

Tyrosine kinase

Taurine

Testosterone

Tetrahydrocannabinol (THC)

Tetrodotoxin

Thapsigargin

Thaumatin

Thiamine (vitamin B1) C12H17ClN4OSHCl

Threonine

Thrombopoietin

Thymidine

Thymine

Triacsin C

Thyroid-stimulating hormone (TSH)

Thyrotropin-releasing hormone (TRH)

Thyroxine (T4)

Tocopherol (Vitamin E)

Topoisomerase

Triiodothyronine (T3)

Transmembrane receptor

Trichostatin A

Trophic hormone

Trypsin

Tryptophan

Tubulin

Tunicamycin

Tyrosine

U[edit]

Ubiquitin

Uracil

Urea

Urease

Uric acid C5H4N4O3

Uridine

V[edit]

Valine

Valinomycin

Vanabins

Vasopressin

Verruculogen

Vitamins (in general)

Vitamin A (retinol)

Vitamin B ()

Vitamin B1 (thiamine)

Vitamin B2 (riboflavin)

Vitamin B3 (niacin or nicotinic acid)

Vitamin B4 (adenine)

Vitamin B5 (pantothenic acid)

Vitamin B6 (pyridoxine or pyridoxamine)

Vitamin B12 (cobalamin)

Vitamin C (ascorbic acid)

Vitamin D (calciferol)

Vitamin E (tocopherol)

Vitamin F

Vitamin H (biotin)

Vitamin K (naphthoquinone)

Vitamin M (folic acid)

W[edit]

Water

Wortmannin

X[edit]

Y[edit]

Xylose

Z[edit]

Zearalenone

Metabolism
From Wikipedia, the free encyclopedia

"Cell metabolism" redirects here. For the journal, see Cell Metabolism.
For the architectural movement, see Metabolism (architecture).
Part of a series on

Biochemistry

Key components

Biomolecules

Metabolism

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Index
Outline

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History
Animal Biochemistry

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Enzymology

Genetics
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List of biochemists
Portals: Biology, MCB

Structure of adenosine triphosphate(ATP), a central intermediate in energy metabolism

Metabolism (from Greek: metabol, "change") is the set of life-sustaining chemical

transformations within the cells of living organisms. Theseenzyme-catalyzed reactions allow
organisms to grow and reproduce, maintain their structures, and respond to their environments. The
word metabolism can also refer to all chemical reactions that occur in living organisms,
includingdigestion and the transport of substances into and between different cells, in which case the
set of reactions within the cells is called intermediary metabolism or intermediate metabolism.
Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter
by way of cellular respiration, and anabolism, thebuilding up of components of cells such
as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes
energy.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical
is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes
are crucial to metabolism because they allow organisms to drive desirable reactions that
require energythat will not occur by themselves, by coupling them to spontaneous reactionsthat
release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes
also allow the regulation of metabolic pathways in response to changes in the cell's environment or
to signals from other cells.
The metabolic system of a particular organism determines which substances it will find nutritious and
which poisonous. For example, some prokaryotes usehydrogen sulfide as a nutrient, yet this gas is
poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an
organism will require, and also affects how it is able to obtain that food.
A striking feature of metabolism is the similarity of the basic metabolic pathways and components
between even vastly different species.[2] For example, the set ofcarboxylic acids that are best known
as the intermediates in the citric acid cycle are present in all known organisms, being found in
species as diverse as the unicellularbacterium Escherichia coli and huge multicellular organisms
like elephants.[3] These striking similarities in metabolic pathways are likely due to their early
appearance inevolutionary history, and their retention because of their efficacy.[4][5]
Contents
[hide]

1Key biochemicals
o

1.1Amino acids and proteins

1.2Lipids

1.3Carbohydrates

1.4Nucleotides

1.5Coenzymes

1.6Minerals and cofactors

2Catabolism
o

2.1Digestion

2.2Energy from organic compounds

3Energy transformations
o

3.1Oxidative phosphorylation

3.2Energy from inorganic compounds

3.3Energy from light

4Anabolism
o

4.1Carbon fixation

4.2Carbohydrates and glycans

4.3Fatty acids, isoprenoids and steroids

4.4Proteins

4.5Nucleotide synthesis and salvage

5Xenobiotics and redox metabolism

6Thermodynamics of living organisms

7Regulation and control

8Evolution

9Investigation and manipulation

10History

11See also

12References

13Further reading

14External links

Key biochemicals[edit]
Further information: Biomolecule, cell (biology) and biochemistry

Structure of a triacylglycerol lipid

Most of the structures that make up animals, plants and microbes are made from three basic classes
of molecule: amino acids, carbohydrates and lipids(often called fats). As these molecules are vital for
life, metabolic reactions either focus on making these molecules during the construction of cells and
tissues, or by breaking them down and using them as a source of energy, by their digestion. These
biochemicals can be joined together to make polymerssuch as DNA and proteins,
essential macromolecules of life.

Name
ofmonomer for
ms

Name
of polymerforms

Examples of polymer
forms

Amino acids

Amino acids

Proteins (also called

polypeptides)

Fibrous
proteins andglobular
proteins

Carbohydrat
es

Monosaccharides

Polysaccharides

Starch, glycogenand cellulo

se

Nucleic acids

Nucleotides

Polynucleotides

DNA and RNA

Type of
molecule

Amino acids and proteins[edit]

Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many
proteins are enzymesthat catalyze the chemical reactions in metabolism. Other proteins have
structural or mechanical functions, such as those that form the cytoskeleton, a system
of scaffolding that maintains the cell shape.[6] Proteins are also important in cell signaling, immune
responses, cell adhesion, active transport across membranes, and the cell cycle.[7] Amino acids also

contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid
cycle (tricarboxylic acid cycle),[8] especially when a primary source of energy, such as glucose, is
scarce, or when cells undergo metabolic stress.[9]

Lipids[edit]
Lipids are the most diverse group of biochemicals. Their main structural uses are as part
of biological membranes both internal and external, such as the cell membrane, or as a source of
energy.[7] Lipids are usually defined as hydrophobic oramphipathic biological molecules but will
dissolve in organic solvents such as benzene or chloroform.[10] The fats are a large group of
compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty
acid esters is called atriacylglyceride.[11] Several variations on this basic structure exist, including
alternate backbones such as sphingosine in thesphingolipids, and hydrophilic groups such
as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids.[12]

Carbohydrates[edit]

Glucose can exist in both a straight-chain and ring form.

Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as
straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill
numerous roles, such as the storage and transport ofenergy (starch, glycogen) and structural
components (cellulose in plants, chitin in animals).[7] The basic carbohydrate units are
called monosaccharides and includegalactose, fructose, and most importantly glucose.
Monosaccharides can be linked together to form polysaccharides in almost limitless ways.[13]

Nucleotides[edit]
The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of
a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous
base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation
through the processes of transcription and protein biosynthesis.[7] This information is protected
by DNA repair mechanisms and propagated through DNA replication. Manyviruses have an RNA
genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA
genome.[14] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can

catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to

a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified
as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.
[15]

Coenzymes[edit]

Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the
extreme left.

Main article: Coenzyme

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of
reactions that involve the transfer offunctional groups of atoms and their bonds within molecules.
[16]
This common chemistry allows cells to use a small set of metabolic intermediates to carry
chemical groups between different reactions.[15]These group-transfer intermediates are
called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme,
which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it.
These coenzymes are therefore continuously made, consumed and then recycled. [17]
One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This
nucleotide is used to transfer chemical energy between different chemical reactions. There is only a
small amount of ATP in cells, but as it is continuously regenerated, the human body can use about
its own weight in ATP per day.[17] ATP acts as a bridge betweencatabolism and anabolism.
Catabolism breaks down molecules and anabolism puts them together. Catabolic reactions generate
ATP and anabolic reactions consume it. It also serves as a carrier of phosphate groups
in phosphorylationreactions.
A vitamin is an organic compound needed in small quantities that cannot be made in cells. In
human nutrition, most vitamins function as coenzymes after modification; for example, all watersoluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.
[18]
Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important
coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove
electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is
then a substrate for any of thereductases in the cell that need to reduce their substrates.
[19]
Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The
NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic
reactions.

Structure of hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in
green. From PDB: 1GZX.

Minerals and cofactors[edit]

Further information: Metal Ions in Life Sciences, Metal metabolism, andbioinorganic chemistry
Inorganic elements play critical roles in metabolism; some are abundant
(e.g. sodium and potassium) while others function at minute concentrations. About 99% of a
mammal's mass is made up of the
elements carbon, nitrogen, calcium, sodium, chlorine, potassium,hydrogen, phosphorus, oxygen and
sulfur.[20] Organic compounds(proteins, lipids and carbohydrates) contain the majority of the carbon
and nitrogen; most of the oxygen and hydrogen is present as water.[20]
The abundant inorganic elements act as ionic electrolytes. The most important ions
are sodium, potassium, calcium, magnesium, chloride,phosphate and the organic ion bicarbonate.
The maintenance of precise ion gradients across cell membranes maintains osmotic
pressure and pH.[21] Ions are also critical for nerve and muscle function, as action potentials in these
tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's
fluid, thecytosol.[22] Electrolytes enter and leave cells through proteins in the cell membrane called ion
channels. For example,muscle contraction depends upon the movement of calcium, sodium and
potassium through ion channels in the cell membrane and T-tubules.[23]
Transition metals are usually present as trace elements in organisms, with zinc and iron being most
abundant of those.[24][25]These metals are used in some proteins as cofactors and are essential for the
activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin.[26] Metal
cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified
during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal

micronutrients are taken up into organisms by specific transporters and bind to storage proteins such
asferritin or metallothionein when not in use.[27][28]

Catabolism[edit]
Catabolism is the set of metabolic processes that break down large molecules. These include
breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the
energy and components needed by anabolic reactions. The exact nature of these catabolic reactions
differ from organism to organism and organisms can be classified based on their sources of energy
and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are
used as a source of energy by organotrophs, while lithotrophs use inorganic substrates
and phototrophscapture sunlight as chemical energy. However, all these different forms of
metabolism depend on redox reactions that involve the transfer of electrons from reduced donor
molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor
molecules such as oxygen, nitrate or sulfate.[29] In animals these reactions involve complex organic
molecules that are broken down to simpler molecules, such as carbon dioxide and water.
In photosyntheticorganisms such as plants and cyanobacteria, these electron-transfer reactions do
not release energy, but are used as a way of storing energy absorbed from sunlight. [30]

Classification of organisms based on

their metabolism

Energ
y
sourc
e

sunligh
t

phot
o-

Prefor
med
molecu
les

che
mo-

Electr organic
on
compo
donor
und

inorgan
ic
compo
und

tro
ph

orga
no-

litho-

Carb
on
sourc
e

organic
compo
und

hete
ro-

inorgan
ic
compo
und

auto-

The most common set of catabolic reactions in animals can be separated into three main stages. In
the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their
smaller components outside cells. Next, these smaller molecules are taken up by cells and
converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some
energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid
cycle and electron transport chain, releasing the energy that is stored by reducing the
coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

Digestion[edit]
Further information: Digestion and gastrointestinal tract
Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must
be broken into their smaller units before they can be used in cell metabolism. Several common
classes of enzymes digest these polymers. These digestive enzymes include proteases that digest
proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple
sugars known as monosaccharides.
Microbes simply secrete digestive enzymes into their surroundings, [31][32] while animals only secrete
these enzymes from specialized cells in their guts.[33] The amino acids or sugars released by these
extracellular enzymes are then pumped into cells by active transport proteins.[34][35]

A simplified outline of the catabolism of proteins,carbohydrates and fats

Energy from organic compounds[edit]

Further information: Cellular respiration, fermentation, carbohydrate catabolism, fat
catabolism and protein catabolism
Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are
usually taken into cells once they have been digested into monosaccharides.[36] Once inside, the
major route of breakdown is glycolysis, where sugars such as glucose andfructose are converted
into pyruvate and some ATP is generated.[37]Pyruvate is an intermediate in several metabolic
pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Although
some more ATP is generated in the citric acid cycle, the most important product is NADH, which is
made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste
product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate
dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose
breakdown is the pentose phosphate pathway, which reduces the coenzymeNADPH and
produces pentose sugars such as ribose, the sugar component of nucleic acids.
Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and
the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the
citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because
carbohydrates contain more oxygen in their structures. Steroids are also broken down by some
bacteria in a process similar to beta oxidation, and this breakdown process involves the release of
significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for
energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes
involved in the cholesterol use pathway(s) have been validated as important during various stages of
the infection lifecycle of M. tuberculosis.[38]

Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and
carbon dioxide as a source of energy.[39] The oxidation pathway starts with the removal of the amino
group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon
skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid
cycle, for example the deamination of glutamate forms -ketoglutarate.[40] The glucogenic amino
acids can also be converted into glucose, through gluconeogenesis (discussed below).[41]

Energy transformations[edit]
Oxidative phosphorylation[edit]
Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion
In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the
protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is
done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron
transport chain. In prokaryotes, these proteins are found in the cell'sinner membrane.[42] These
proteins use the energy released from passing electrons from reduced molecules like NADH
ontooxygen to pump protons across a membrane.[43]

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in
black.

Pumping protons out of the mitochondria creates a proton concentration differenceacross the
membrane and generates an electrochemical gradient.[44] This force drives protons back into the
mitochondrion through the base of an enzyme calledATP synthase. The flow of protons makes the
stalk subunit rotate, causing the active site of the synthase domain to change shape and
phosphorylate adenosine diphosphate turning it into ATP.[17]

Energy from inorganic compounds[edit]

Further information: Microbial metabolism and nitrogen cycle

Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the
oxidation of inorganic compounds. These organisms can usehydrogen,[45] reduced sulfur compounds
(such as sulfide, hydrogen sulfide andthiosulfate),[1] ferrous iron (FeII)[46] or ammonia[47] as sources of
reducing power and they gain energy from the oxidation of these compounds with electron acceptors
such as oxygen or nitrite.[48] These microbial processes are important in global biogeochemical
cycles such asacetogenesis, nitrification and denitrification and are critical for soil fertility.[49][50]

Energy from light[edit]

Further information: Phototroph, photophosphorylation, chloroplast
The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur
bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into
organic compounds, as part of photosynthesis, which is discussed below. The energy capture and
carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and
green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation
and the fermentation of organic compounds.[51][52]
In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as
it involves the storage of energy as a proton concentration gradient. This proton motive force then
drives ATP synthesis.[17] The electrons needed to drive this electron transport chain come from lightgathering proteins called photosynthetic reaction centres orrhodopsins. Reaction centers are classed
into two types depending on the type of photosynthetic pigment present, with most photosynthetic
bacteria only having one type, while plants and cyanobacteria have two. [53]
In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from
water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex,
which uses their energy to pump protons across thethylakoid membrane in the chloroplast.[30] These
protons move back through the membrane as they drive the ATP synthase, as before. The electrons
then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for
use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.[54]

Anabolism[edit]
Further information: Anabolism
Anabolism is the set of constructive metabolic processes where the energy released by catabolism
is used to synthesize complex molecules. In general, the complex molecules that make up cellular
structures are constructed step-by-step from small and simple precursors. Anabolism involves three
basic stages. First, the production of precursors such as amino
acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms
using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such
as proteins, polysaccharides, lipids and nucleic acids.

Organisms differ in how many of the molecules in their cells they can construct for
themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as
polysaccharides and proteins from simple molecules likecarbon dioxide and water. Heterotrophs, on
the other hand, require a source of more complex substances, such as monosaccharides and amino
acids, to produce these complex molecules. Organisms can be further classified by ultimate source
of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas
chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.

Carbon fixation[edit]
Further information: Photosynthesis, carbon fixation and chemosynthesis

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide(CO2). In plants,
cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste
product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres,
as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into
glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of theCalvin
Benson cycle.[55] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon
fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin
cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO 2 into
other compounds first, as adaptations to deal with intense sunlight and dry conditions. [56]
In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon
dioxide can be fixed by the Calvin Benson cycle, a reversed citric acid cycle,[57] or the carboxylation
of acetyl-CoA.[58][59] Prokaryotic chemoautotrophs also fix CO2 through the Calvin Benson cycle, but
use energy from inorganic compounds to drive the reaction. [60]

Carbohydrates and glycans[edit]

Further information: Gluconeogenesis, glyoxylate cycle, glycogenesis and glycosylation
In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such
as glucose and then used to assemble polysaccharides such as starch. The generation
of glucose from compounds like pyruvate, lactate, glycerol,glycerate 3-phosphate and amino acids is

called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a

series of intermediates, many of which are shared with glycolysis.[37] However, this pathway is not
simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is
important as it allows the formation and breakdown of glucose to be regulated separately, and
prevents both pathways from running simultaneously in a futile cycle.[61][62]
Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in
these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot
convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic
machinery.[63] As a result, after long-term starvation, vertebrates need to produce ketone bodies from
fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. [64]In
other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate
cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation
of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose.[63][65]
Polysaccharides and glycans are made by the sequential addition of monosaccharides
by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate
glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. As any of
the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can
have straight or branched structures.[66] The polysaccharides produced can have structural or
metabolic functions themselves, or be transferred to lipids and proteins by enzymes
called oligosaccharyltransferases.[67][68]

Fatty acids, isoprenoids and steroids[edit]

Further information: Fatty acid synthesis, steroid metabolism

Simplified version of the steroid synthesis pathway with the intermediates isopentenyl
pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP)
andsqualene shown. Some intermediates are omitted for clarity.

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The
acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it
to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The
enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty
acid synthase reactions are carried out by a single multifunctional type I protein, [69] while in
plantplastids and bacteria separate type II enzymes perform each step in the pathway.[70][71]
Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest
class of plantnatural products.[72] These compounds are made by the assembly and modification
of isoprene units donated from the reactive precursors isopentenyl pyrophosphate anddimethylallyl
pyrophosphate.[73] These precursors can be made in different ways. In animals and archaea,
the mevalonate pathway produces these compounds from acetyl-CoA,[74] while in plants and bacteria
the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[73][75]One
important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the
isoprene units are joined together to make squalene and then folded up and formed into a set of
rings to make lanosterol.[76] Lanosterol can then be converted into other steroids such
as cholesteroland ergosterol.[76][77]

Proteins[edit]

Further information: Protein biosynthesis, amino acid synthesis

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants
can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so
nine essential amino acids must be obtained from food.[7] Some simple parasites, such as the
bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly
from their hosts.[78] All amino acids are synthesized from intermediates in glycolysis, the citric acid
cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino
acid synthesis depends on the formation of the appropriate alpha-keto acid, which is
then transaminated to form an amino acid.[79]
Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each
different protein has a unique sequence of amino acid residues: this is its primary structure. Just as
the letters of the alphabet can be combined to form an almost endless variety of words, amino acids
can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino
acids that have been activated by attachment to a transfer RNA molecule through an esterbond.
This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by
an aminoacyl tRNA synthetase.[80] This aminoacyl-tRNA is then a substrate for the ribosome, which
joins the amino acid onto the elongating protein chain, using the sequence information in
a messenger RNA.[81]

Nucleotide synthesis and salvage[edit]

Further information: Nucleotide salvage, pyrimidine biosynthesis, and purine metabolism
Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require
large amounts of metabolic energy.[82] Consequently, most organisms have efficient systems to
salvage preformed nucleotides.[82][83] Purines are synthesized as nucleosides (bases attached
to ribose).[84] Both adenine and guanine are made from the precursor
nucleoside inosine monophosphate, which is synthesized using atoms from the amino
acids glycine, glutamine, and aspartic acid, as well as formate transferred from
the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the
base orotate, which is formed from glutamine and aspartate.[85]

Xenobiotics and redox metabolism[edit]

Further information: Xenobiotic metabolism, drug metabolism, Alcohol metabolism and antioxidants
All organisms are constantly exposed to compounds that they cannot use as foods and would be
harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging
compounds are called xenobiotics.[86]Xenobiotics such as synthetic drugs, natural
poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these
include cytochrome P450 oxidases,[87] UDP-glucuronosyltransferases,[88] and glutathione Stransferases.[89] This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I)
and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble

xenobiotic can then be pumped out of cells and in multicellular organisms may be further
metabolized before being excreted (phase III). In ecology, these reactions are particularly important
in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills.
[90]
Many of these microbial reactions are shared with multicellular organisms, but due to the incredible
diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics
than multicellular organisms, and can degrade even persistent organic pollutants such
as organochloride compounds.[91]
A related problem for aerobic organisms is oxidative stress.[92] Here, processes including oxidative
phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen
species such as hydrogen peroxide.[93] These damaging oxidants are removed
by antioxidant metabolites such as glutathione and enzymes such as catalases andperoxidases.[94][95]

Thermodynamics of living organisms[edit]

Further information: Biological thermodynamics
Living organisms must obey the laws of thermodynamics, which describe the transfer of heat
and work. The second law of thermodynamics states that in any closed system, the amount
of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to
contradict this law, life is possible as all organisms are open systems that exchange matter and
energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative
systems that maintain their state of high complexity by causing a larger increase in the entropy of
their environments.[96] The metabolism of a cell achieves this by coupling the spontaneous
processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms,
metabolism maintains order by creating disorder.[97]

Regulation and control[edit]

Further information: Metabolic pathway, metabolic control analysis, hormone, regulatory enzymes,
and cell signaling
As the environments of most organisms are constantly changing, the reactions of metabolism must
be finely regulated to maintain a constant set of conditions within cells, a condition
called homeostasis.[98][99] Metabolic regulation also allows organisms to respond to signals and
interact actively with their environments.[100] Two closely linked concepts are important for
understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a
pathway is how its activity is increased and decreased in response to signals. Secondly,
the control exerted by this enzyme is the effect that these changes in its activity have on the overall
rate of the pathway (the flux through the pathway).[101] For example, an enzyme may show large
changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a
metabolic pathway, then this enzyme is not involved in the control of the pathway.[102]

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts
many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma
membrane and influx of glucose (3),glycogen synthesis (4), glycolysis (5) and fatty acidsynthesis (6).

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway selfregulates to respond to changes in the levels of substrates or products; for example, a decrease in
the amount of product can increase the flux through the pathway to compensate.[101] This type of
regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway.
[103]
Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to
signals from other cells. These signals are usually in the form of soluble messengers such
as hormones andgrowth factors and are detected by specific receptors on the cell surface.[104] These
signals are then transmitted inside the cell bysecond messenger systems that often involved
the phosphorylation of proteins.[105]
A very well understood example of extrinsic control is the regulation of glucose metabolism by the
hormone insulin.[106] Insulin is produced in response to rises in blood glucose levels. Binding of the
hormone to insulin receptors on cells then activates a cascade ofprotein kinases that cause the cells
to take up glucose and convert it into storage molecules such as fatty acids andglycogen.[107] The
metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down
glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a
reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase.
Insulin causes glycogen synthesis by activatingprotein phosphatases and producing a decrease in
the phosphorylation of these enzymes.[108]

Evolution[edit]
Further information: Molecular evolution and phylogenetics

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are
colored blue, eukaryotes red, andarchaea green. Relative positions of some of the phyla included are shown
around the tree.

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle,
are present in all three domains of living things and were present in the last universal ancestor.[3]
[109]
This universal ancestral cell was prokaryotic and probably amethanogen that had extensive
amino acid, nucleotide, carbohydrate and lipid metabolism. [110][111] The retention of these ancient
pathways during laterevolution may be the result of these reactions having been an optimal solution
to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle
producing their end products highly efficiently and in a minimal number of steps. [4][5]Mutation changes
that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for
whom the mutation occurs.[112] The first pathways of enzyme-based metabolism may have been parts
of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA
world.[113]
Many models have been proposed to describe the mechanisms by which novel metabolic pathways
evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the
duplication and then divergence of entire pathways as well as the recruitment of pre-existing
enzymes and their assembly into a novel reaction pathway.[114] The relative importance of these
mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to
have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with
novel functions created from pre-existing steps in the pathway.[115] An alternative model comes from
studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that
enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different
metabolic pathways (evident in the MANET database)[116] These recruitment processes result in an
evolutionary enzymatic mosaic.[117] A third possibility is that some parts of metabolism might exist as
"modules" that can be reused in different pathways and perform similar functions on different
molecules.[118]

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic
functions. For example, in some parasites metabolic processes that are not essential for survival are
lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from
the host.[119] Similar reduced metabolic capabilities are seen inendosymbiotic organisms.[120]

Investigation and manipulation[edit]

Further information: Protein methods, proteomics, metabolomics and metabolic network modelling

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red
squares and the interactions between them as black lines.

Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic

pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and
cellular levels, which define the paths from precursors to final products by identifying radioactively
labelled intermediates and products.[121] The enzymes that catalyze these chemical reactions can
then be purified and their kineticsand responses to inhibitors investigated. A parallel approach is to
identify the small molecules in a cell or tissue; the complete set of these molecules is called
the metabolome. Overall, these studies give a good view of the structure and function of simple
metabolic pathways, but are inadequate when applied to more complex systems such as the
metabolism of a complete cell.[122]
An idea of the complexity of the metabolic networks in cells that contain thousands of different
enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites
to the right: the sequences of genomes provide lists containing anything up to 45,000 genes.
[123]
However, it is now possible to use this genomic data to reconstruct complete networks of
biochemical reactions and produce more holistic mathematical models that may explain and predict
their behavior.[124] These models are especially powerful when used to integrate the pathway and

metabolite data obtained through classical methods with data on gene

expression from proteomicand DNA microarray studies.[125] Using these techniques, a model of
human metabolism has now been produced, which will guide future drug discovery and biochemical
research.[126] These models are now used in network analysis, to classify human diseases into groups
that share common proteins or metabolites.[127][128]
Bacterial metabolic networks are a striking example of bow-tie[129][130][131] organization, an architecture
able to input a wide range of nutrients and produce a large variety of products and complex
macromolecules using a relatively few intermediate common currencies.
A major technological application of this information is metabolic engineering. Here, organisms such
as yeast, plants orbacteria are genetically modified to make them more useful in biotechnology and
aid the production of drugs such asantibiotics or industrial chemicals such as 1,3propanediol and shikimic acid.[132] These genetic modifications usually aim to reduce the amount of
energy used to produce the product, increase yields and reduce the production of wastes. [133]

History[edit]
Further information: History of biochemistry and history of molecular biology

Santorio Santorio in his steelyard balance, fromArs de statica medicina, first published 1614

The term metabolism is derived from the Greek "Metabolismos" for "change", or
"overthrow".[134] The first documented references of metabolism were made by Ibn al-Nafis in his
1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the
Prophet's Biography) which included the following phrase "Both the body and its parts are in a
continuous state of dissolution and nourishment, so they are inevitably undergoing permanent
change."[135] The history of the scientific study of metabolism spans several centuries and has moved
from examining whole animals in early studies, to examining individual metabolic reactions in
modern biochemistry. The first controlled experiments in human metabolism were published
by Santorio Santorio in 1614 in his book Ars de statica medicina.[136] He described how he weighed
himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that
most of the food he took in was lost through what he called "insensible perspiration".

In these early studies, the mechanisms of these metabolic processes had not been identified and
a vital force was thought to animate living tissue.[137] In the 19th century, when studying
thefermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was
catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic
fermentation is an act correlated with the life and organization of the yeast cells, not with the death
or putrefaction of the cells."[138] This discovery, along with the publication by Friedrich Whler in 1828
of a paper on the chemical synthesis ofurea,[139] and is notable for being the first organic compound
prepared from wholly inorganic precursors. This proved that the organic compounds and chemical
reactions found in cells were no different in principle than any other part of chemistry.
It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that
separated the study of the chemical reactions of metabolism from the biological study of cells, and
marked the beginnings of biochemistry.[140] The mass of biochemical knowledge grew rapidly
throughout the early 20th century. One of the most prolific of these modern biochemists was Hans
Krebs who made huge contributions to the study of metabolism.[141] He discovered the urea cycle and
later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.[142][65] Modern
biochemical research has been greatly aided by the development of new techniques such
as chromatography, X-ray diffraction, NMR spectroscopy,radioisotopic labelling, electron
microscopy and molecular dynamics simulations. These techniques have allowed the discovery and
detailed analysis of the many molecules and metabolic pathways in cells.

Metabolism
From Wikipedia, the free encyclopedia

"Cell metabolism" redirects here. For the journal, see Cell Metabolism.
For the architectural movement, see Metabolism (architecture).
Part of a series on

Biochemistry

Key components

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Index
Outline

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History
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Portals: Biology, MCB

Structure of adenosine triphosphate(ATP), a central intermediate in energy metabolism

Metabolism (from Greek: metabol, "change") is the set of life-sustaining chemical

transformations within the cells of living organisms. Theseenzyme-catalyzed reactions allow
organisms to grow and reproduce, maintain their structures, and respond to their environments. The
word metabolism can also refer to all chemical reactions that occur in living organisms,
includingdigestion and the transport of substances into and between different cells, in which case the
set of reactions within the cells is called intermediary metabolism or intermediate metabolism.
Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter
by way of cellular respiration, and anabolism, thebuilding up of components of cells such
as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes
energy.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical
is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes
are crucial to metabolism because they allow organisms to drive desirable reactions that
require energythat will not occur by themselves, by coupling them to spontaneous reactionsthat
release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes
also allow the regulation of metabolic pathways in response to changes in the cell's environment or
to signals from other cells.
The metabolic system of a particular organism determines which substances it will find nutritious and
which poisonous. For example, some prokaryotes usehydrogen sulfide as a nutrient, yet this gas is
poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an
organism will require, and also affects how it is able to obtain that food.
A striking feature of metabolism is the similarity of the basic metabolic pathways and components
between even vastly different species.[2] For example, the set ofcarboxylic acids that are best known
as the intermediates in the citric acid cycle are present in all known organisms, being found in
species as diverse as the unicellularbacterium Escherichia coli and huge multicellular organisms
like elephants.[3] These striking similarities in metabolic pathways are likely due to their early
appearance inevolutionary history, and their retention because of their efficacy.[4][5]
Contents

[hide]

1Key biochemicals
o

1.1Amino acids and proteins

1.2Lipids

1.3Carbohydrates

1.4Nucleotides

1.5Coenzymes

1.6Minerals and cofactors

2Catabolism
o

2.1Digestion

2.2Energy from organic compounds

3Energy transformations
o

3.1Oxidative phosphorylation

3.2Energy from inorganic compounds

3.3Energy from light

4Anabolism
o

4.1Carbon fixation

4.2Carbohydrates and glycans

4.3Fatty acids, isoprenoids and steroids

4.4Proteins

4.5Nucleotide synthesis and salvage

5Xenobiotics and redox metabolism

6Thermodynamics of living organisms

7Regulation and control

8Evolution

9Investigation and manipulation

10History

11See also

12References

13Further reading

14External links

Key biochemicals[edit]
Further information: Biomolecule, cell (biology) and biochemistry

Structure of a triacylglycerol lipid

Most of the structures that make up animals, plants and microbes are made from three basic classes
of molecule: amino acids, carbohydrates and lipids(often called fats). As these molecules are vital for
life, metabolic reactions either focus on making these molecules during the construction of cells and
tissues, or by breaking them down and using them as a source of energy, by their digestion. These
biochemicals can be joined together to make polymerssuch as DNA and proteins,
essential macromolecules of life.

Type of
molecule

Name
ofmonomer for
ms

Name
of polymerforms

Examples of polymer
forms

Amino acids

Amino acids

Proteins (also called

Fibrous

polypeptides)

proteins andglobular
proteins

Carbohydrat
es

Monosaccharides

Polysaccharides

Starch, glycogenand cellulo

se

Nucleic acids

Nucleotides

Polynucleotides

DNA and RNA

Amino acids and proteins[edit]

Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many
proteins are enzymesthat catalyze the chemical reactions in metabolism. Other proteins have
structural or mechanical functions, such as those that form the cytoskeleton, a system
of scaffolding that maintains the cell shape.[6] Proteins are also important in cell signaling, immune
responses, cell adhesion, active transport across membranes, and the cell cycle.[7] Amino acids also
contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid
cycle (tricarboxylic acid cycle),[8] especially when a primary source of energy, such as glucose, is
scarce, or when cells undergo metabolic stress.[9]

Lipids[edit]
Lipids are the most diverse group of biochemicals. Their main structural uses are as part
of biological membranes both internal and external, such as the cell membrane, or as a source of
energy.[7] Lipids are usually defined as hydrophobic oramphipathic biological molecules but will
dissolve in organic solvents such as benzene or chloroform.[10] The fats are a large group of
compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty
acid esters is called atriacylglyceride.[11] Several variations on this basic structure exist, including
alternate backbones such as sphingosine in thesphingolipids, and hydrophilic groups such
as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids.[12]

Carbohydrates[edit]

Glucose can exist in both a straight-chain and ring form.

Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as
straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill
numerous roles, such as the storage and transport ofenergy (starch, glycogen) and structural
components (cellulose in plants, chitin in animals).[7] The basic carbohydrate units are
called monosaccharides and includegalactose, fructose, and most importantly glucose.
Monosaccharides can be linked together to form polysaccharides in almost limitless ways.[13]

Nucleotides[edit]
The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of
a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous
base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation
through the processes of transcription and protein biosynthesis.[7] This information is protected
by DNA repair mechanisms and propagated through DNA replication. Manyviruses have an RNA
genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA
genome.[14] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can
catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to
a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified
as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.
[15]

Coenzymes[edit]

Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the
extreme left.

Main article: Coenzyme

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of
reactions that involve the transfer offunctional groups of atoms and their bonds within molecules.
[16]
This common chemistry allows cells to use a small set of metabolic intermediates to carry
chemical groups between different reactions.[15]These group-transfer intermediates are
called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme,
which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it.
These coenzymes are therefore continuously made, consumed and then recycled. [17]

One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This
nucleotide is used to transfer chemical energy between different chemical reactions. There is only a
small amount of ATP in cells, but as it is continuously regenerated, the human body can use about
its own weight in ATP per day.[17] ATP acts as a bridge betweencatabolism and anabolism.
Catabolism breaks down molecules and anabolism puts them together. Catabolic reactions generate
ATP and anabolic reactions consume it. It also serves as a carrier of phosphate groups
in phosphorylationreactions.
A vitamin is an organic compound needed in small quantities that cannot be made in cells. In
human nutrition, most vitamins function as coenzymes after modification; for example, all watersoluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.
[18]
Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important
coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove
electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is
then a substrate for any of thereductases in the cell that need to reduce their substrates.
[19]
Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The
NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic
reactions.

Structure of hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in
green. From PDB: 1GZX.

Minerals and cofactors[edit]

Further information: Metal Ions in Life Sciences, Metal metabolism, andbioinorganic chemistry
Inorganic elements play critical roles in metabolism; some are abundant
(e.g. sodium and potassium) while others function at minute concentrations. About 99% of a
mammal's mass is made up of the

elements carbon, nitrogen, calcium, sodium, chlorine, potassium,hydrogen, phosphorus, oxygen and
sulfur.[20] Organic compounds(proteins, lipids and carbohydrates) contain the majority of the carbon
and nitrogen; most of the oxygen and hydrogen is present as water.[20]
The abundant inorganic elements act as ionic electrolytes. The most important ions
are sodium, potassium, calcium, magnesium, chloride,phosphate and the organic ion bicarbonate.
The maintenance of precise ion gradients across cell membranes maintains osmotic
pressure and pH.[21] Ions are also critical for nerve and muscle function, as action potentials in these
tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's
fluid, thecytosol.[22] Electrolytes enter and leave cells through proteins in the cell membrane called ion
channels. For example,muscle contraction depends upon the movement of calcium, sodium and
potassium through ion channels in the cell membrane and T-tubules.[23]
Transition metals are usually present as trace elements in organisms, with zinc and iron being most
abundant of those.[24][25]These metals are used in some proteins as cofactors and are essential for the
activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin.[26] Metal
cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified
during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal
micronutrients are taken up into organisms by specific transporters and bind to storage proteins such
asferritin or metallothionein when not in use.[27][28]

Catabolism[edit]
Catabolism is the set of metabolic processes that break down large molecules. These include
breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the
energy and components needed by anabolic reactions. The exact nature of these catabolic reactions
differ from organism to organism and organisms can be classified based on their sources of energy
and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are
used as a source of energy by organotrophs, while lithotrophs use inorganic substrates
and phototrophscapture sunlight as chemical energy. However, all these different forms of
metabolism depend on redox reactions that involve the transfer of electrons from reduced donor
molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor
molecules such as oxygen, nitrate or sulfate.[29] In animals these reactions involve complex organic
molecules that are broken down to simpler molecules, such as carbon dioxide and water.
In photosyntheticorganisms such as plants and cyanobacteria, these electron-transfer reactions do
not release energy, but are used as a way of storing energy absorbed from sunlight. [30]

Classification of organisms based on

their metabolism

Energ
y

sunligh
t

phot
o-

tro

sourc
e

Prefor
med
molecu
les

organic
compo
und
Electr
on
donor inorgan
ic
compo
und

Carb
on
sourc
e

che
mo-

orga
no-

litho-

ph

organic
compo
und

hete
ro-

inorgan
ic
compo
und

auto-

The most common set of catabolic reactions in animals can be separated into three main stages. In
the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their
smaller components outside cells. Next, these smaller molecules are taken up by cells and
converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some
energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid
cycle and electron transport chain, releasing the energy that is stored by reducing the
coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

Digestion[edit]
Further information: Digestion and gastrointestinal tract
Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must
be broken into their smaller units before they can be used in cell metabolism. Several common
classes of enzymes digest these polymers. These digestive enzymes include proteases that digest
proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple
sugars known as monosaccharides.

Microbes simply secrete digestive enzymes into their surroundings, [31][32] while animals only secrete
these enzymes from specialized cells in their guts.[33] The amino acids or sugars released by these
extracellular enzymes are then pumped into cells by active transport proteins.[34][35]

A simplified outline of the catabolism of proteins,carbohydrates and fats

Energy from organic compounds[edit]

Further information: Cellular respiration, fermentation, carbohydrate catabolism, fat
catabolism and protein catabolism
Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are
usually taken into cells once they have been digested into monosaccharides.[36] Once inside, the
major route of breakdown is glycolysis, where sugars such as glucose andfructose are converted
into pyruvate and some ATP is generated.[37]Pyruvate is an intermediate in several metabolic
pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Although
some more ATP is generated in the citric acid cycle, the most important product is NADH, which is
made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste
product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate
dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose
breakdown is the pentose phosphate pathway, which reduces the coenzymeNADPH and
produces pentose sugars such as ribose, the sugar component of nucleic acids.
Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and
the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the
citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because
carbohydrates contain more oxygen in their structures. Steroids are also broken down by some
bacteria in a process similar to beta oxidation, and this breakdown process involves the release of
significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for
energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes

involved in the cholesterol use pathway(s) have been validated as important during various stages of
the infection lifecycle of M. tuberculosis.[38]
Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and
carbon dioxide as a source of energy.[39] The oxidation pathway starts with the removal of the amino
group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon
skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid
cycle, for example the deamination of glutamate forms -ketoglutarate.[40] The glucogenic amino
acids can also be converted into glucose, through gluconeogenesis (discussed below).[41]

Energy transformations[edit]
Oxidative phosphorylation[edit]
Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion
In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the
protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is
done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron
transport chain. In prokaryotes, these proteins are found in the cell'sinner membrane.[42] These
proteins use the energy released from passing electrons from reduced molecules like NADH
ontooxygen to pump protons across a membrane.[43]

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in
black.

Pumping protons out of the mitochondria creates a proton concentration differenceacross the
membrane and generates an electrochemical gradient.[44] This force drives protons back into the
mitochondrion through the base of an enzyme calledATP synthase. The flow of protons makes the
stalk subunit rotate, causing the active site of the synthase domain to change shape and
phosphorylate adenosine diphosphate turning it into ATP.[17]

Energy from inorganic compounds[edit]

Further information: Microbial metabolism and nitrogen cycle

Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the
oxidation of inorganic compounds. These organisms can usehydrogen,[45] reduced sulfur compounds
(such as sulfide, hydrogen sulfide andthiosulfate),[1] ferrous iron (FeII)[46] or ammonia[47] as sources of
reducing power and they gain energy from the oxidation of these compounds with electron acceptors
such as oxygen or nitrite.[48] These microbial processes are important in global biogeochemical
cycles such asacetogenesis, nitrification and denitrification and are critical for soil fertility.[49][50]

Energy from light[edit]

Further information: Phototroph, photophosphorylation, chloroplast
The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur
bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into
organic compounds, as part of photosynthesis, which is discussed below. The energy capture and
carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and
green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation
and the fermentation of organic compounds.[51][52]
In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as
it involves the storage of energy as a proton concentration gradient. This proton motive force then
drives ATP synthesis.[17] The electrons needed to drive this electron transport chain come from lightgathering proteins called photosynthetic reaction centres orrhodopsins. Reaction centers are classed
into two types depending on the type of photosynthetic pigment present, with most photosynthetic
bacteria only having one type, while plants and cyanobacteria have two. [53]
In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from
water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex,
which uses their energy to pump protons across thethylakoid membrane in the chloroplast.[30] These
protons move back through the membrane as they drive the ATP synthase, as before. The electrons
then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for
use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.[54]

Anabolism[edit]
Further information: Anabolism
Anabolism is the set of constructive metabolic processes where the energy released by catabolism
is used to synthesize complex molecules. In general, the complex molecules that make up cellular
structures are constructed step-by-step from small and simple precursors. Anabolism involves three
basic stages. First, the production of precursors such as amino
acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms
using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such
as proteins, polysaccharides, lipids and nucleic acids.

Organisms differ in how many of the molecules in their cells they can construct for
themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as
polysaccharides and proteins from simple molecules likecarbon dioxide and water. Heterotrophs, on
the other hand, require a source of more complex substances, such as monosaccharides and amino
acids, to produce these complex molecules. Organisms can be further classified by ultimate source
of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas
chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.

Carbon fixation[edit]
Further information: Photosynthesis, carbon fixation and chemosynthesis

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide(CO2). In plants,
cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste
product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres,
as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into
glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of theCalvin
Benson cycle.[55] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon
fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin
cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO 2 into
other compounds first, as adaptations to deal with intense sunlight and dry conditions. [56]
In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon
dioxide can be fixed by the Calvin Benson cycle, a reversed citric acid cycle,[57] or the carboxylation
of acetyl-CoA.[58][59] Prokaryotic chemoautotrophs also fix CO2 through the Calvin Benson cycle, but
use energy from inorganic compounds to drive the reaction. [60]

Carbohydrates and glycans[edit]

Further information: Gluconeogenesis, glyoxylate cycle, glycogenesis and glycosylation
In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such
as glucose and then used to assemble polysaccharides such as starch. The generation
of glucose from compounds like pyruvate, lactate, glycerol,glycerate 3-phosphate and amino acids is

called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a

series of intermediates, many of which are shared with glycolysis.[37] However, this pathway is not
simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is
important as it allows the formation and breakdown of glucose to be regulated separately, and
prevents both pathways from running simultaneously in a futile cycle.[61][62]
Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in
these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot
convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic
machinery.[63] As a result, after long-term starvation, vertebrates need to produce ketone bodies from
fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. [64]In
other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate
cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation
of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose.[63][65]
Polysaccharides and glycans are made by the sequential addition of monosaccharides
by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate
glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. As any of
the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can
have straight or branched structures.[66] The polysaccharides produced can have structural or
metabolic functions themselves, or be transferred to lipids and proteins by enzymes
called oligosaccharyltransferases.[67][68]

Fatty acids, isoprenoids and steroids[edit]

Further information: Fatty acid synthesis, steroid metabolism

Simplified version of the steroid synthesis pathway with the intermediates isopentenyl
pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP)
andsqualene shown. Some intermediates are omitted for clarity.

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The
acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it
to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The
enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty
acid synthase reactions are carried out by a single multifunctional type I protein, [69] while in
plantplastids and bacteria separate type II enzymes perform each step in the pathway.[70][71]
Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest
class of plantnatural products.[72] These compounds are made by the assembly and modification
of isoprene units donated from the reactive precursors isopentenyl pyrophosphate anddimethylallyl
pyrophosphate.[73] These precursors can be made in different ways. In animals and archaea,
the mevalonate pathway produces these compounds from acetyl-CoA,[74] while in plants and bacteria
the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[73][75]One
important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the
isoprene units are joined together to make squalene and then folded up and formed into a set of
rings to make lanosterol.[76] Lanosterol can then be converted into other steroids such
as cholesteroland ergosterol.[76][77]

Proteins[edit]

Further information: Protein biosynthesis, amino acid synthesis

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants
can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so
nine essential amino acids must be obtained from food.[7] Some simple parasites, such as the
bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly
from their hosts.[78] All amino acids are synthesized from intermediates in glycolysis, the citric acid
cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino
acid synthesis depends on the formation of the appropriate alpha-keto acid, which is
then transaminated to form an amino acid.[79]
Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each
different protein has a unique sequence of amino acid residues: this is its primary structure. Just as
the letters of the alphabet can be combined to form an almost endless variety of words, amino acids
can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino
acids that have been activated by attachment to a transfer RNA molecule through an esterbond.
This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by
an aminoacyl tRNA synthetase.[80] This aminoacyl-tRNA is then a substrate for the ribosome, which
joins the amino acid onto the elongating protein chain, using the sequence information in
a messenger RNA.[81]

Nucleotide synthesis and salvage[edit]

Further information: Nucleotide salvage, pyrimidine biosynthesis, and purine metabolism
Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require
large amounts of metabolic energy.[82] Consequently, most organisms have efficient systems to
salvage preformed nucleotides.[82][83] Purines are synthesized as nucleosides (bases attached
to ribose).[84] Both adenine and guanine are made from the precursor
nucleoside inosine monophosphate, which is synthesized using atoms from the amino
acids glycine, glutamine, and aspartic acid, as well as formate transferred from
the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the
base orotate, which is formed from glutamine and aspartate.[85]

Xenobiotics and redox metabolism[edit]

Further information: Xenobiotic metabolism, drug metabolism, Alcohol metabolism and antioxidants
All organisms are constantly exposed to compounds that they cannot use as foods and would be
harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging
compounds are called xenobiotics.[86]Xenobiotics such as synthetic drugs, natural
poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these
include cytochrome P450 oxidases,[87] UDP-glucuronosyltransferases,[88] and glutathione Stransferases.[89] This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I)
and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble

xenobiotic can then be pumped out of cells and in multicellular organisms may be further
metabolized before being excreted (phase III). In ecology, these reactions are particularly important
in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills.
[90]
Many of these microbial reactions are shared with multicellular organisms, but due to the incredible
diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics
than multicellular organisms, and can degrade even persistent organic pollutants such
as organochloride compounds.[91]
A related problem for aerobic organisms is oxidative stress.[92] Here, processes including oxidative
phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen
species such as hydrogen peroxide.[93] These damaging oxidants are removed
by antioxidant metabolites such as glutathione and enzymes such as catalases andperoxidases.[94][95]

Thermodynamics of living organisms[edit]

Further information: Biological thermodynamics
Living organisms must obey the laws of thermodynamics, which describe the transfer of heat
and work. The second law of thermodynamics states that in any closed system, the amount
of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to
contradict this law, life is possible as all organisms are open systems that exchange matter and
energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative
systems that maintain their state of high complexity by causing a larger increase in the entropy of
their environments.[96] The metabolism of a cell achieves this by coupling the spontaneous
processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms,
metabolism maintains order by creating disorder.[97]

Regulation and control[edit]

Further information: Metabolic pathway, metabolic control analysis, hormone, regulatory enzymes,
and cell signaling
As the environments of most organisms are constantly changing, the reactions of metabolism must
be finely regulated to maintain a constant set of conditions within cells, a condition
called homeostasis.[98][99] Metabolic regulation also allows organisms to respond to signals and
interact actively with their environments.[100] Two closely linked concepts are important for
understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a
pathway is how its activity is increased and decreased in response to signals. Secondly,
the control exerted by this enzyme is the effect that these changes in its activity have on the overall
rate of the pathway (the flux through the pathway).[101] For example, an enzyme may show large
changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a
metabolic pathway, then this enzyme is not involved in the control of the pathway.[102]

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts
many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma
membrane and influx of glucose (3),glycogen synthesis (4), glycolysis (5) and fatty acidsynthesis (6).

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway selfregulates to respond to changes in the levels of substrates or products; for example, a decrease in
the amount of product can increase the flux through the pathway to compensate.[101] This type of
regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway.
[103]
Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to
signals from other cells. These signals are usually in the form of soluble messengers such
as hormones andgrowth factors and are detected by specific receptors on the cell surface.[104] These
signals are then transmitted inside the cell bysecond messenger systems that often involved
the phosphorylation of proteins.[105]
A very well understood example of extrinsic control is the regulation of glucose metabolism by the
hormone insulin.[106] Insulin is produced in response to rises in blood glucose levels. Binding of the
hormone to insulin receptors on cells then activates a cascade ofprotein kinases that cause the cells
to take up glucose and convert it into storage molecules such as fatty acids andglycogen.[107] The
metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down
glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a
reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase.
Insulin causes glycogen synthesis by activatingprotein phosphatases and producing a decrease in
the phosphorylation of these enzymes.[108]

Evolution[edit]
Further information: Molecular evolution and phylogenetics

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are
colored blue, eukaryotes red, andarchaea green. Relative positions of some of the phyla included are shown
around the tree.

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle,
are present in all three domains of living things and were present in the last universal ancestor.[3]
[109]
This universal ancestral cell was prokaryotic and probably amethanogen that had extensive
amino acid, nucleotide, carbohydrate and lipid metabolism. [110][111] The retention of these ancient
pathways during laterevolution may be the result of these reactions having been an optimal solution
to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle
producing their end products highly efficiently and in a minimal number of steps. [4][5]Mutation changes
that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for
whom the mutation occurs.[112] The first pathways of enzyme-based metabolism may have been parts
of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA
world.[113]
Many models have been proposed to describe the mechanisms by which novel metabolic pathways
evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the
duplication and then divergence of entire pathways as well as the recruitment of pre-existing
enzymes and their assembly into a novel reaction pathway.[114] The relative importance of these
mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to
have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with
novel functions created from pre-existing steps in the pathway.[115] An alternative model comes from
studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that
enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different
metabolic pathways (evident in the MANET database)[116] These recruitment processes result in an
evolutionary enzymatic mosaic.[117] A third possibility is that some parts of metabolism might exist as
"modules" that can be reused in different pathways and perform similar functions on different
molecules.[118]

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic
functions. For example, in some parasites metabolic processes that are not essential for survival are
lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from
the host.[119] Similar reduced metabolic capabilities are seen inendosymbiotic organisms.[120]

Investigation and manipulation[edit]

Further information: Protein methods, proteomics, metabolomics and metabolic network modelling

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red
squares and the interactions between them as black lines.

Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic

pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and
cellular levels, which define the paths from precursors to final products by identifying radioactively
labelled intermediates and products.[121] The enzymes that catalyze these chemical reactions can
then be purified and their kineticsand responses to inhibitors investigated. A parallel approach is to
identify the small molecules in a cell or tissue; the complete set of these molecules is called
the metabolome. Overall, these studies give a good view of the structure and function of simple
metabolic pathways, but are inadequate when applied to more complex systems such as the
metabolism of a complete cell.[122]
An idea of the complexity of the metabolic networks in cells that contain thousands of different
enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites
to the right: the sequences of genomes provide lists containing anything up to 45,000 genes.
[123]
However, it is now possible to use this genomic data to reconstruct complete networks of
biochemical reactions and produce more holistic mathematical models that may explain and predict
their behavior.[124] These models are especially powerful when used to integrate the pathway and

metabolite data obtained through classical methods with data on gene

expression from proteomicand DNA microarray studies.[125] Using these techniques, a model of
human metabolism has now been produced, which will guide future drug discovery and biochemical
research.[126] These models are now used in network analysis, to classify human diseases into groups
that share common proteins or metabolites.[127][128]
Bacterial metabolic networks are a striking example of bow-tie[129][130][131] organization, an architecture
able to input a wide range of nutrients and produce a large variety of products and complex
macromolecules using a relatively few intermediate common currencies.
A major technological application of this information is metabolic engineering. Here, organisms such
as yeast, plants orbacteria are genetically modified to make them more useful in biotechnology and
aid the production of drugs such asantibiotics or industrial chemicals such as 1,3propanediol and shikimic acid.[132] These genetic modifications usually aim to reduce the amount of
energy used to produce the product, increase yields and reduce the production of wastes. [133]

History[edit]
Further information: History of biochemistry and history of molecular biology

Santorio Santorio in his steelyard balance, fromArs de statica medicina, first published 1614

The term metabolism is derived from the Greek "Metabolismos" for "change", or
"overthrow".[134] The first documented references of metabolism were made by Ibn al-Nafis in his
1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the
Prophet's Biography) which included the following phrase "Both the body and its parts are in a
continuous state of dissolution and nourishment, so they are inevitably undergoing permanent
change."[135] The history of the scientific study of metabolism spans several centuries and has moved
from examining whole animals in early studies, to examining individual metabolic reactions in
modern biochemistry. The first controlled experiments in human metabolism were published
by Santorio Santorio in 1614 in his book Ars de statica medicina.[136] He described how he weighed
himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that
most of the food he took in was lost through what he called "insensible perspiration".

In these early studies, the mechanisms of these metabolic processes had not been identified and
a vital force was thought to animate living tissue.[137] In the 19th century, when studying
thefermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was
catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic
fermentation is an act correlated with the life and organization of the yeast cells, not with the death
or putrefaction of the cells."[138] This discovery, along with the publication by Friedrich Whler in 1828
of a paper on the chemical synthesis ofurea,[139] and is notable for being the first organic compound
prepared from wholly inorganic precursors. This proved that the organic compounds and chemical
reactions found in cells were no different in principle than any other part of chemistry.
It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that
separated the study of the chemical reactions of metabolism from the biological study of cells, and
marked the beginnings of biochemistry.[140] The mass of biochemical knowledge grew rapidly
throughout the early 20th century. One of the most prolific of these modern biochemists was Hans
Krebs who made huge contributions to the study of metabolism.[141] He discovered the urea cycle and
later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.[142][65] Modern
biochemical research has been greatly aided by the development of new techniques such
as chromatography, X-ray diffraction, NMR spectroscopy,radioisotopic labelling, electron
microscopy and molecular dynamics simulations. These techniques have allowed the discovery and
detailed analysis of the many molecules and metabolic pathways in cells.

Molecular biology
From Wikipedia, the free encyclopedia
Part of a series on

Biochemistry

Key components

Biomolecules

Metabolism

Glossary

Index
Outline

History and topics

History
Animal Biochemistry

Cell Biology

Bioinformatics

Enzymology

Genetics
Immunology

Molecular Biology

Plant Biochemistry

Structural Biology

Branches of biochemistry

List of biochemists
Portals: Biology, MCB

Molecular biology /mlkjlr/ concerns the molecular basis of biologicalactivity between the
various systems of a cell, including the interactions between DNA, RNA and proteins and
their biosynthesis, as well as the regulation of these interactions. Writing in Nature in 1961, William
Astburydescribed molecular biology as:
"...not so much a technique as an approach, an approach from the viewpoint of the so-called basic
sciences with the leading idea of searching below the large-scale manifestations of classical biology
for the corresponding molecular plan. It is concerned particularly with the forms of biological
molecules and [...] is predominantly three-dimensional and structuralwhich does not mean,
however, that it is merely a refinement of morphology. It must at the same time inquire into genesis
and function."[1]
Contents
[hide]

1Relationship to other biological sciences

2Techniques of molecular biology

o

2.1Molecular cloning

2.2Polymerase chain reaction (PCR)

2.3Gel electrophoresis

2.4Macromolecule blotting and probing

2.4.1Southern blotting

2.4.2Northern blotting

2.4.3Western blotting

2.4.4Eastern blotting

2.5Microarrays

2.6Allele-specific oligonucleotide

2.7Antiquated technologies

3History

4Clinical significance

5See also

6References

7Further reading

8External links

Relationship to other biological sciences[edit]

Schematic relationship betweenbiochemistry, genetics and molecular biology

Researchers in molecular biology use specific techniques native to molecular biology but
increasingly combine these with techniques and ideas from genetics andbiochemistry. There is not a
defined line between these disciplines. The figure to the right is a schematic that depicts one
possible view of the relationship between the fields:

Biochemistry is the study of the chemical substances and vital processes occurring in
live organisms. Biochemists focus heavily on the role, function, and structure of biomolecules.
The study of the chemistry behind biological processes and the synthesis of biologically active
molecules are examples ofbiochemistry.

Genetics is the study of the effect of genetic differences on organisms. This can often be
inferred by the absence of a normal component (e.g. one gene). The study of "mutants"
organisms which lack one or more functional components with respect to the so-called "wild
type" or normal phenotype. Genetic interactions (epistasis) can often confound simple
interpretations of such "knockout" studies.

Molecular biology is the study of molecular underpinnings of the processes

of replication, transcription, translation, and cell function. The central dogma of molecular
biology where genetic material is transcribed into RNA and then translated into protein, despite
being an oversimplified picture of molecular biology, still provides a good starting point for
understanding the field. This picture, however, is undergoing revision in light of emerging novel
roles for RNA.

Much of the work in molecular biology is quantitative, and recently much work has been done at the
interface of molecular biology and computer science in bioinformatics and computational biology. As
of the early 2000s, the study of gene structure and function, molecular genetics, has been among
the most prominent sub-field of molecular biology.
Increasingly many other loops of biology focus on molecules, either directly studying their
interactions in their own right such as in cell biology and developmental biology, or indirectly, where
the techniques of molecular biology are used to infer historical attributes of populations or species,
as in fields in evolutionary biology such as population genetics andphylogenetics. There is also a
long tradition of studying biomolecules "from the ground up" in biophysics.

Techniques of molecular biology[edit]

Since the late 1950s and early 1960s, molecular biologists have learned to characterize, isolate, and
manipulate the molecular components of cells and organisms. These components include DNA, the
repository of genetic information; RNA, a close relative of DNA whose functions range from serving
as a temporary working copy of DNA to actual structural and enzymatic functions as well as a
functional and structural part of the translational apparatus, the ribosome; and proteins, the major
structural and enzymatic type of molecule in cells.
For more extensive list on protein methods, see protein methods. For more extensive list on nucleic
acid methods, seenucleic acid methods.

Molecular cloning[edit]
Main article: Molecular cloning
One of the most basic techniques of molecular biology to study protein function is molecular cloning.
In this technique, DNA coding for a protein of interest is cloned (using PCR and/or restriction
enzymes) into a plasmid (known as an expression vector). A vector has 3 distinctive features: an
origin of replication, a multiple cloning site (MCS), and a selective marker (usually antibiotic
resistance). The origin of replication will have promoter regions upstream from
the replication/transcriptionstart site.
This plasmid can be inserted into either bacterial or animal cells. Introducing DNA into bacterial cells
can be done bytransformation (via uptake of naked DNA), conjugation (via cell-cell contact) or
by transduction (via viral vector). Introducing DNA into eukaryotic cells, such as animal cells, by
physical or chemical means is called transfection. Several different transfection techniques are
available, such as calcium phosphate transfection, electroporation, microinjection and liposome
transfection. DNA can also be introduced into eukaryotic cells using viruses or bacteria as carriers,
the latter is sometimes called bactofection and in particular uses Agrobacterium tumefaciens. The
plasmid may be integrated into the genome, resulting in a stable transfection, or may remain
independent of the genome, called transient transfection.

In either case, DNA coding for a protein of interest is now inside a cell, and the protein can now be
expressed. A variety of systems, such as inducible promoters and specific cell-signaling factors, are
available to help express the protein of interest at high levels. Large quantities of a protein can then
be extracted from the bacterial or eukaryotic cell. The protein can be tested for enzymatic activity
under a variety of situations, the protein may be crystallized so its tertiary structure can be studied,
or, in the pharmaceutical industry, the activity of new drugs against the protein can be studied.

Polymerase chain reaction (PCR)[edit]

Main article: Polymerase chain reaction
Polymerase chain reaction is an extremely versatile technique for copying DNA. In brief, PCR allows
a specific DNA sequence to be copied or modified in predetermined ways. The reaction is extremely
powerful and under perfect conditions could amplify 1 DNA molecule to become 1.07 Billion
molecules in less than 2 hours. The PCR technique can be used to introduce restriction enzyme
sites to ends of DNA molecules, or to mutate (change) particular bases of DNA, the latter is a
method referred to as site-directed mutagenesis. PCR can also be used to determine whether a
particular DNA fragment is found in a cDNA library. PCR has many variations, like reverse
transcription PCR (RT-PCR) for amplification of RNA, and, more recently, quantitative PCR which
allow for quantitative measurement of DNA or RNA molecules.

Gel electrophoresis[edit]
Main article: Gel electrophoresis
Gel electrophoresis is one of the principal tools of molecular biology. The basic principle is that DNA,
RNA, and proteins can all be separated by means of an electric field and size. In agarose gel
electrophoresis, DNA and RNA can be separated on the basis of size by running the DNA through an
electrically charged agarose gel. Proteins can be separated on the basis of size by using an SDSPAGE gel, or on the basis of size and their electric charge by using what is known as a 2D gel
electrophoresis.

Macromolecule blotting and probing[edit]

The terms northern, western and eastern blotting are derived from what initially was a molecular
biology joke that played on the term Southern blotting, after the technique described by Edwin
Southern for the hybridisation of blotted DNA. Patricia Thomas, developer of the RNA blot which
then became known as the northern blot, actually didn't use the term.[2] Further combinations of
these techniques produced such terms as southwesterns (protein-DNA
hybridizations), northwesterns (to detect protein-RNA interactions) and farwesterns (protein-protein
interactions), all of which are presently found in the literature.
Southern blotting[edit]
Main article: Southern blot

Named after its inventor, biologist Edwin Southern, the Southern blot is a method for probing for the
presence of a specific DNA sequence within a DNA sample. DNA samples before or after restriction
enzyme (restriction endonuclease) digestion are separated by gel electrophoresis and then
transferred to a membrane by blotting via capillary action. The membrane is then exposed to a
labeled DNA probe that has a complement base sequence to the sequence on the DNA of interest.
Most original protocols used radioactive labels, however non-radioactive alternatives are now
available. Southern blotting is less commonly used in laboratory science due to the capacity of other
techniques, such as PCR, to detect specific DNA sequences from DNA samples. These blots are still
used for some applications, however, such as measuring transgenecopy number in transgenic mice,
or in the engineering of gene knockout embryonic stem cell lines.
Northern blotting[edit]
Main article: Northern blot
The northern blot is used to study the expression patterns of a specific type of RNA molecule as
relative comparison among a set of different samples of RNA. It is essentially a combination
of denaturing RNA gel electrophoresis, and a blot. In this process RNA is separated based on size
and is then transferred to a membrane that is then probed with a labeledcomplement of a sequence
of interest. The results may be visualized through a variety of ways depending on the label used;
however, most result in the revelation of bands representing the sizes of the RNA detected in
sample. The intensity of these bands is related to the amount of the target RNA in the samples
analyzed. The procedure is commonly used to study when and how much gene expression is
occurring by measuring how much of that RNA is present in different samples. It is one of the most
basic tools for determining at what time, and under what conditions, certain genes are expressed in
living tissues.
Western blotting[edit]
Main article: Western blot
Antibodies to most proteins can be created by injecting small amounts of the protein into an animal
such as a mouse, rabbit, sheep, or donkey (polyclonal antibodies) or produced in cell culture
(monoclonal antibodies). These antibodies can be used for a variety of analytical and preparative
techniques.
In western blotting, proteins are first separated by size, in a thin gel sandwiched between two glass
plates in a technique known as SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel
electrophoresis). The proteins in the gel are then transferred to a polyvinylidene fluoride (PVDF),
nitrocellulose, nylon, or other support membrane. This membrane can then be probed with solutions
of antibodies. Antibodies that specifically bind to the protein of interest can then be visualized by a
variety of techniques, including colored products, chemiluminescence, or autoradiography. Often,
the antibodies are labeled with enzymes. When a chemiluminescent substrate is exposed to
the enzyme it allows detection. Using western blotting techniques allows not only detection but also
quantitative analysis.

Analogous methods to western blotting can be used to directly stain specific proteins in
live cells or tissue sections. However, these immunostaining methods, such as FISH, are used more
often in cell biology research.
Eastern blotting[edit]
Main article: Eastern blot
The Eastern blotting technique is used to detect post-translational modification of proteins.[3] Proteins
blotted on to the PVDF or nitrocellulose membrane are probed for modifications using specific
substrates.

Microarrays[edit]
Main article: DNA microarray
A DNA microarray is a collection of spots attached to a solid support such as a microscope
slide where each spot contains one or more single-stranded DNA oligonucleotide fragment. Arrays
make it possible to put down large quantities of very small (100 micrometre diameter) spots on a
single slide. Each spot has a DNA fragment molecule that is complementary to a single DNA
sequence (similar to Southern blotting). A variation of this technique allows the gene expression of
an organism at a particular stage in development to be qualified (expression profiling). In this
technique the RNA in a tissue is isolated and converted to labeled cDNA. This cDNA is then
hybridized to the fragments on the array and visualization of the hybridization can be done. Since
multiple arrays can be made with exactly the same position of fragments they are particularly useful
for comparing the gene expression of two different tissues, such as a healthy and cancerous tissue.
Also, one can measure what genes are expressed and how that expression changes with time or
with other factors. For instance, the common baker's yeast, Saccharomyces cerevisiae, contains
about 7000 genes; with a microarray, one can measure qualitatively how each gene is expressed,
and how that expression changes, for example, with a change in temperature. There are many
different ways to fabricate microarrays; the most common are silicon chips, microscope slides with
spots of ~ 100 micrometre diameter, custom arrays, and arrays with larger spots on porous
membranes (macroarrays). There can be anywhere from 100 spots to more than 10,000 on a given
array.
Arrays can also be made with molecules other than DNA. For example, an antibody array can be
used to determine whatproteins or bacteria are present in a blood sample.

Allele-specific oligonucleotide[edit]
Allele-specific oligonucleotide (ASO) is a technique that allows detection of single base mutations
without the need for PCR or gel electrophoresis. Short (20-25 nucleotides in length), labeled probes
are exposed to the non-fragmented target DNA. Hybridization occurs with high specificity due to the
short length of the probes and even a single base change will hinder hybridization. The target DNA is
then washed and the labeled probes that didn't hybridize are removed. The target DNA is then
analyzed for the presence of the probe via radioactivity or fluorescence. In this experiment, as in

most molecular biology techniques, a control must be used to ensure successful experimentation.
The Illumina Methylation Assay is an example of a method that takes advantage of the ASO
technique to measure one base pair differences in sequence. [citation needed]

Antiquated technologies[edit]
In molecular biology, procedures and technologies are continually being developed and older
technologies abandoned. For example, before the advent of DNA gel
electrophoresis (agarose or polyacrylamide), the size of DNA molecules was typically determined by
rate sedimentation in sucrose gradients, a slow and labor-intensive technique requiring expensive
instrumentation; prior to sucrose gradients, viscometry was used.
Aside from their historical interest, it is often worth knowing about older technology, as it is
occasionally useful to solve another new problem for which the newer technique is inappropriate.

History[edit]
Main article: History of molecular biology
While molecular biology was established in the 1930s, the term was coined by Warren Weaver in
1938. Weaver was the director of Natural Sciences for the Rockefeller Foundation at the time and
believed that biology was about to undergo a period of significant change given recent advances in
fields such as X-ray crystallography. He therefore channeled significant amounts of (Rockefeller
Institute) money into biological fields.

Clinical significance[edit]
Clinical research and medical therapies arising from molecular biology are partly covered
under gene therapy[citation needed]. The use of molecular biology or molecular cell biology approaches in
medicine is now called molecular medicine. Molecular biology also plays important role in
understanding formations, actions, regulations of various parts of cells which can be used efficiently
for targeting new drugs, diagnosis of disease, physiology of the Cell.

Multi-state modeling of biomolecules

From Wikipedia, the free encyclopedia

Multi-state modeling of biomolecules refers to a series of techniques used to represent and

compute the behaviour ofbiological molecules or complexes that can adopt a large number of
possible functional states.

Biological signaling systems often rely on complexes of biological macromolecules that can undergo
several functionally significant modifications that are mutually compatible. Thus, they can exist in a
very large number of functionally different states. Modeling such multi-state systems poses two
problems: The problem of how to describe and specify a multi-state system (the "specification
problem") and the problem of how to use a computer to simulate the progress of the system over
time (the "computation problem"). To address the specification problem, modelers have in recent
years moved away from explicit specification of all possible states, and towards rulebased formalisms that allow for implicit model specification, including the -calculus, [1] BioNetGen,[2][3]
[4][5]
the Allosteric Network Compiler[6] and others.[7][8] To tackle the computation problem, they have
turned to particle-based methods that have in many cases proved more computationally efficient
than population-based methods based on ordinary differential equations, partial differential
equations, or the Gillespie stochastic simulation algorithm.[9][10] Given current computing technology,
particle-based methods are sometimes the only possible option. Particle-based simulators further fall
into two categories: Non-spatial simulators such as StochSim,[11] DYNSTOC,[12]RuleMonkey,[9][13] and
NFSim[14] and spatial simulators, including Meredys,[15] SRSim[16][17] and MCell.[18][19][20] Modelers can thus
choose from a variety of tools; the best choice depending on the particular problem. Development of
faster and more powerful methods is ongoing, promising the ability to simulate ever more complex
signaling processes in the future.
Contents
[hide]

1Introduction
o

1.1Multi-state biomolecules in signal transduction

1.2Examples of combinatorial explosion

1.3Specification vs computation

2The specification problem

o

2.1Explicit specification

2.2Rule-based model specification

3The computation problem

o

3.1Population-based rule evaluation

3.2Particle-based rule evaluation

3.3Non-spatial particle-based methods

3.4Spatial particle-based methods

4Examples of multi-state models in biology

5See also

6References

Introduction[edit]
Multi-state biomolecules in signal transduction [edit]
In living cells, signals are processed by networks of proteins that can act as complex computational
devices.[21] These networks rely on the ability of single proteins to exist in a variety of functionally
different states achieved through multiple mechanisms, including posttranslational
modifications, ligand binding, conformational change, or formation of newcomplexes.[21][22][23]
[24]
Similarly, nucleic acids can undergo a variety of transformations, including protein binding, binding
of other nucleic acids, conformational change and DNA methylation.
In addition, several types of modifications can co-exist, exerting a combined influence on a biological
macromolecule at any given time. Thus, a biomolecule or complex of biomolecules can often adopt a
very large number of functionally distinct states. The number of states scales exponentially with the
number of possible modifications, a phenomenon known as "combinatorial explosion".[24] This is of
concern for computational biologists who model or simulate such biomolecules, because it raises
questions about how such large numbers of states can be represented and simulated.

Examples of combinatorial explosion[edit]

Biological signaling networks incorporate a wide array of reversible interactions, post-translational
modifications andconformational changes. Furthermore, it is common for a protein to be composed
of several - identical or nonidentical -subunits, and for several proteins and/or nucleic acid species to
assemble into larger complexes. A molecular species with several of those features can therefore
exist in a large number of possible states.
For instance, it has been estimated that the yeast scaffold protein Ste5 can be a part of 25666
unique protein complexes.[22]In E. coli, chemotaxis receptors of four different kinds interact in groups
of three, and each individual receptor can exist in at least two possible conformations and has up to
eight methylation sites,[23] resulting in billions of potential states. The proteinkinase CaMKII is
a dodecamer of twelve catalytic subunits,[25] arranged in two hexameric rings.[26] Each subunit can
exist in at least two distinct conformations, and each subunit features various phosphorylation and
ligand binding sites. A recent model[27] incorporated conformational states, two phosphorylation sites
and two modes of binding calcium/calmodulin, for a total of around one billion possible states per
hexameric ring. A model of coupling of the EGF receptor to a MAP kinasecascade presented by
Danos and colleagues[28] accounts for
distinct molecular species, yet the authors note
several points at which the model could be further extended. A more recent model of ErbB receptor
signalling even accounts for more than one googol (

) distinct molecular species.[29] The

problem of combinatorial explosion is also relevant tosynthetic biology, with a recent model of a
relatively simple synthetic eukaryotic gene circuit featuring 187 species and 1165reactions.[30]
Of course, not all of the possible states of a multi-state molecule or complex will necessarily be
populated. Indeed, in systems where the number of possible states is far greater than that of
molecules in the compartment (e.g. the cell), they cannot be. In some cases, empirical information
can be used to rule out certain states if, for instance, some combinations of features are
incompatible. In the absence of such information, however, all possible states need to be
considered a priori. In such cases, computational modeling can be used to uncover to what extent
the different states are populated.
The existence (or potential existence) of such large numbers of molecular species is
a combinatorial phenomenon: It arises from a relatively small set of features or modifications (such
as post-translational modification or complex formation) that combine to dictate the state of the entire
molecule or complex, in the same way that the existence of just a few choices in acoffee
shop (small, medium or large, with or without milk, decaf or not, extra shot of espresso) quickly leads
to a large number of possible beverages (24 in this case; each additional binary choice will double
that number). Although it is difficult for us to grasp the total numbers of possible combinations, it is
usually not conceptually difficult to understand the (much smaller) set of features or modifications
and the effect each of them has on the function of the biomolecule. The rate at which a molecule
undergoes a particular reaction will usually depend mainly on a single feature or a small subset of
features. It is the presence or absence of those features that dictates the reaction rate. The reaction
rate is the same for two molecules that differ only in features which do not affect this reaction. Thus,
the number of parameters will be much smaller than the number of reactions. (In the coffee shop
example, adding an extra shot of espresso will cost 40 cent, no matter what size the beverage is and
whether or not it has milk in it). It is such "local rules" that are usually discovered in laboratory
experiments. Thus, a multi-state model can be conceptualised in terms of combinations of modular
features and local rules. This means that even a model that can account for a vast number of
molecular species and reactions is not necessarily conceptually complex.

Specification vs computation[edit]

Figure 1: An overview of tools discussed here that are used for the rule-based specification and particle-based
evaluation (spatial or non-spatial) of multi-state biomolecules.

The combinatorial complexity of signaling systems involving multi-state proteins poses two kinds of
problems. The first problem is concerned with how such a system can be specified; i.e. how a
modeler can specify all complexes, all changes those complexes undergo and all parameters and
conditions governing those changes in a robust and efficient way. This problem is called the
"specification problem". The second problem concerns computation. It asks questions about whether
a combinatorially complex model, once specified, is computationally tractable, given the large
number of states and the even larger number of possible transitions between states, whether it can
be stored electronically, and whether it can be evaluated in a reasonable amount of computing time.
This problem is called the "computation problem". Among the approaches that have been proposed
to tackle combinatorial complexity in multi-state modeling, some are mainly concerned with
addressing the specification problem, some are focused on finding effective methods of
computation. Some tools address both specification and computation. The sections below discuss
rule-based approaches to the specification problem and particle-based approaches to solving the
computation problem. A list of the tools discussed here is presented in Figure 1. A comprehensive
overview and discussion of various tools available for multi-state modeling can be found in Chylek et
al.[31]

The specification problem[edit]

Explicit specification[edit]
The most nave way of specifying, e.g., a protein in a biological model is to specify each of its states
explicitly and use each of them as a molecular species in a simulation framework that allows
transitions from state to state. For instance, if a protein can be ligand-bound or not, exist in
two conformational states (e.g. open or closed) and be located in two possible subcellular areas
(e.g. cytosolic or membrane-bound), then the eight possible resulting states can be explicitly
enumerated as:

bound, open, cytosol

bound, open, membrane

bound, closed, cytosol

bound, closed, membrane

unbound, open, cytosol

unbound, open, membrane

unbound, closed, cytosol

unbound, closed, membrane

Enumerating all possible states is a lengthy and potentially error-prone process. For macromolecular
complexes that can adopt multiple states, enumerating each state quickly becomes tedious, if not

impossible. Moreover, the addition of a single additional modification or feature to the model of the
complex under investigation will double the number of possible states (if the modification is binary),
and it will more than double the number of transitions that need to be specified.

Rule-based model specification[edit]

It is clear that an explicit description, which lists all possible molecular species (including all their
possible states), all possible reactions or transitions these species can undergo, and all parameters
governing these reactions, very quickly becomes unwieldy as the complexity of the biological system
increases. Modelers have therefore looked for implicit, rather than explicit, ways of specifying a
biological signaling system. An implicit description is one that groups reactions and parameters that
apply to many types of molecular species into one reaction template. It might also add a set of
conditions that govern reaction parameters, i.e. the likelihood or rate at which a reaction occurs, or
whether it occurs at all. Only properties of the molecule or complex that matter to a given reaction
(either affecting the reaction or being affected by it) are explicitly mentioned, and all other properties
are ignored in the specification of the reaction.
For instance, the rate of ligand dissociation from a protein might depend on the conformational state
of the protein, but not on its subcellular localization. An implicit description would therefore list two
dissociation processes (with different rates, depending on conformational state), but would ignore
attributes referring to subcellular localization, because they do not affect the rate of ligand
dissociation, nor are they affected by it. This specification rule has been summarized as "Don't care,
don't write".[28]
Since it is not written in terms of reactions, but in terms of more general "reaction rules"
encompassing sets of reactions, this kind of specification is often called "rule-based".[4] This
description of the system in terms of modular rules relies on the assumption that only a subset of
features or attributes are relevant for a particular reaction rule. Where this assumption holds, a set of
reactions can be coarse-grained into one reaction rule. This coarse-graining preserves the important
properties of the underlying reactions. For instance, if the reactions are based on chemical kinetics,
so are the rules derived from them.
Many rule-based specification methods exist. In general, the specification of a model is a separate
task from the execution of the simulation. Therefore, among the existing rule-based model
specification systems,[4] some concentrate on model specification only, allowing the user to then
export the specified model into a dedicated simulation engine. However, many solutions to the
specification problem also contain a method of interpreting the specified model. [3] This is done by
providing a method to simulate the model or a method to convert it into a form that can be used for
simulations in other programs.
An early rule-based specification method is the -calculus,[1] a process algebra that can be used to
encode macromolecules with internal states and binding sites and to specify rules by which they
interact. A review of is provided by Danos et al.[28]The -calculus is merely concerned with providing
a language to encode multi-state models, not with interpreting the models themselves. A simulator
compatible with Kappa is KaSim.[32][33]

BioNetGen is a software suite that provides both specification and simulation capacities. [2][3][4][5] Rulebased models can be written down using a specified syntax, the BioNetGen language (BNGL). [4] The
underlying concept is to represent biochemical systems as graphs, where molecules are
represented as nodes (or collections of nodes) and chemical bonds as edges. A reaction rule, then,
corresponds to a graph rewriting rule.[3] BNGL provides a syntax for specifying these graphs and the
associated rules as structured strings.[4] BioNetGen can then use these rules to generate ordinary
differential equations (ODEs) to describe each biochemical reaction. Alternatively, it can generate a
list of all possible species and reactions in SBML,[34][35] which can then be exported to simulation
software packages that can read SBML. One can also make use of BioNetGen's own ODE-based
simulation software and its capability to generate reactions on-the-fly during a stochastic simulation.
[5]
In addition, a model specified in BNGL can be read by other simulation software, such as
DYNSTOC,[12] RuleMonkey,[13] and NFSim.[14]
Another tool that generates full reaction networks from a set of rules is the Allosteric Network
Compiler (ANC).[6]Conceptually, ANC sees molecules as allosteric devices with a Monod-WymanChangeux (MWC) type regulation mechanism,[36] whose interactions are governed by their internal
state, as well as by external modifications. A very useful feature of ANC is that it automatically
computes dependent parameters, thereby imposing thermodynamic correctness.[37]
An extension of the -calculus is provided by React(C).[38] The authors of React C show that it can
express the stochastic calculus.[39] They also provide a stochastic simulation algorithm based on
the Gillespie stochastic algorithm [40] for models specified in React(C).[38]
ML-Rules[41] is similar to React(C), but provides the added possibility of nesting: A component
species of the model, with all its attributes, can be part of a higher-order component species. This
enables ML-Rules to capture multi-level models that can bridge the gap between, for instance, a
series of biochemical processes and the macroscopic behaviour of a whole cell or group of cells. For
instance, Maus et al. have provided a proof-of-concept model of cell division in fission yeast that
includes cyclin/cdc2 binding and activation, pheromone secretion and diffusion, cell division and
movement of cells.[41]Models specified in ML-Rules can be simulated using the James II simulation
framework.[42] A similar nested language to represent multi-level biological systems has been
proposed by Oury and Plotkin.[43]
Yang et al.[8] have proposed a specification formalism based on finite automata. Models specified in
their Molecular Finite Automata (MFA) framework can then be used to generate and simulate a
system of ODEs or for stochastic simulation using a kinetic Monte Carlo algorithm.
Some rule-based specification systems and their associated network generation and simulation tools
have been designed to accommodate spatial heterogeneity, in order to allow for the realistic
simulation of interactions within biological compartments. For instance, the Simmune project [44]
[45]
includes a spatial component: Users can specify their multi-state biomolecules and interactions
within membranes or compartments of arbitrary shape. The reaction volume is then divided into
interfacing voxels, and a separate reaction network generated for each of these subvolumes.
The Stochastic Simulator Compiler (SSC)[46] allows for rule-based, modular specification of
interacting biomolecules in regions of arbitrarily complex geometries. Again, the system is

represented using graphs, with chemical interactions or diffusion events formalised as graphrewriting rules.[46] The compiler then generates the entire reaction network before launching a
stochastic reaction-diffusion algorithm.
A different approach is taken by PySB,[47] where model specification is embedded in the programming
language Python. A model (or part of a model) is represented as a Python programme. This allows
users to store higher-order biochemical processes such as catalysis or polymerisation as macros
and re-use them as needed. The models can be simulated and analysed using Python libraries, but
PySB models can also be exported into BNGL,[4] kappa,[1] and SBML.[34]
Models involving multi-state and multi-component species can also be specified in Level 3 of the
Systems Biology Markup Language (SBML) [34] using the multi package. A draft specification is
available,[48] and software support is under development.
Thus, by only considering states and features important for a particular reaction, rule-based model
specification eliminates the need to explicitly enumerate every possible molecular state that can
undergo a similar reaction, and thereby allows for efficient specification.

The computation problem[edit]

When running simulations on a biological model, any simulation software evaluates a set of rules,
starting from a specified set of initial conditions, and usually iterating through a series of time steps
until a specified end time. One way to classify simulation algorithms is by looking at the level of
analysis at which the rules are applied: they can be population-based, single-particle-based or
hybrid.

Population-based rule evaluation[edit]

In Population-based rule evaluation, rules are applied to populations. All molecules of the
same species in the same state are pooled together. Application of a specific rule reduces or
increases the size of one of the pools, possibly at the expense of another.
Some of the best-known classes of simulation approaches in computational biology belong to the
population-based family, including those based on the numerical integration of ordinary and partial
differential equations and the Gillespie stochastic simulation algorithm.
Differential equations describe changes in molecular concentrations over time in a deterministic
manner. Simulations based on differential equations usually do not attempt to solve those equations
analytically, but employ a suitable numerical solver.
The stochastic Gillespie algorithm changes the composition of pools of molecules through a
progression of randomnessreaction events, the probability of which is computed from reaction rates
and from the numbers of molecules, in accordance with the stochastic master equation.[40]

In population-based approaches, one can think of the system being modeled as being in a given
state at any given time point, where a state is defined according to the nature and size of the
populated pools of molecules. This means that the space of all possible states can become very
large. With some simulation methods implementing numerical integration of ordinary and partial
differential equations or the Gillespie stochastic algorithm, all possible pools of molecules and the
reactions they undergo are defined at the start of the simulation, even if they are empty. Such
"generate-first" methods[4]scale poorly with increasing numbers of molecular states.[49] For instance, it
has recently been estimated that even for a simple model of CaMKII with just 6 states per subunits
and 10 subunits, it would take 290 years to generate the entire reaction network on a 2.54 GHz
Intel Xeon processor.[50] In addition, the model generation step in generate-first methods does not
necessarily terminate, for instance when the model includes assembly of proteins into complexes of
arbitrarily large size, such as actin filaments. In these cases, a termination condition needs to be
specified by the user.[3][5]
Even if a large reaction system can be successfully generated, its simulation using population-based
rule evaluation can run into computational limits. In a recent study, a powerful computer was shown
to be unable to simulate a protein with more than 8 phosphorylation sites (
phosphorylation states) using ordinary differential equations.[14]
Methods have been proposed to reduce the size of the state space. One is to consider only the
states adjacent to the present state (i.e. the states that can be reached within the next iteration) at
each time point. This eliminates the need for enumerating all possible states at the beginning.
Instead, reactions are generated "on-the-fly"[4] at each iteration. These methods are available both for
stochastic and deterministic algorithms. These methods still rely on the definition of an (albeit
reduced) reaction network - in contrast to the "network-free" methods discussed below.
Even with "on-the-fly" network generation, networks generated for population-based rule evaluation
can become quite large, and thus difficult - if not impossible - to handle computationally. An
alternative approach is provided by particle-based rule evaluation.

Particle-based rule evaluation[edit]

Figure 2: Principles of particle-based modeling. In particle-based modeling, each particle is tracked individually
through the simulation. At any point, a particle only "sees" the rules that apply to it. This figure follows two
molecular particles (one of type A in red, one of type B in blue) through three steps in a hypothetical simulation
following a simple set of rules (given on the right). At each step, the rules that potentially apply to the particle
under consideration are highlighted in that particle's colour.

In particle-based (sometimes called "agent-based") simulations, proteins, nucleic acids,

macromolecular complexes or small molecules are represented as individual software objects, and
their progress is tracked through the course of the entire simulation.[51] Because particle-based rule
evaluation keeps track of individual particles rather than populations, it comes at a higher
computational cost when modeling systems with a high total number of particles, but a small number
of kinds (or pools) of particles.[51] In cases of combinatorial complexity, however, the modeling of
individual particles is an advantage because, at any given point in the simulation, only existing
molecules, their states and the reactions they can undergo need to be considered. Particle-based
rule evaluation does not require the generation of complete or partial reaction networks at the start of
the simulation or at any other point in the simulation and is therefore called "network-free".
This method reduces the complexity of the model at the simulation stage, and thereby saves time
and computational power.[9] A detailed discussion of the computational cost of population-based
versus particle-based methods is summarised in a recent study by Hogg et al. [10] The simulation
follows each particle, and at each simulation step, a particle only "sees" the reactions (or rules) that
apply to it. This depends on the state of the particle and, in some implementation, on the states of its
neighbours in a holoenzyme or complex. As the simulation proceeds, the states of particles are
updated according to the rules that are fired. Figure 2 illustrates the process of particle-based
modeling using a simple system with three molecules of type A and one molecular tetramer of type
B, which goes through three simulation steps following a simple set of rules.

Some particle-based simulation packages use an ad-hoc formalism for specification of reactants,
parameters and rules. Others can read files in a recognised rule-based specification format such as
BNGL.[4]

Non-spatial particle-based methods[edit]

StochSim[11][52] is a particle-based stochastic simulator used mainly to model chemical reactions and
other molecular transitions. The algorithm used in StochSim is different from the more widely known
Gillespie stochastic algorithm[40] in that it operates on individual entities, not entity pools, making it
particle-based rather than population-based.
In StochSim, each molecular species can be equipped with a number of binary
state flags representing a particular modification. Reactions can be made dependent on a set of
state flags set to particular values. In addition, the outcome of a reaction can include a state flag
being changed. Moreover, entities can be arranged in geometric arrays (for instance, for
holoenzymes consisting of several subunits), and reactions can be "neighbor-sensitive", i.e. the
probability of a reaction for a given entity is affected by the value of a state flag on a neighboring
entity. These properties make StochSim ideally suited to modeling multi-state molecules arranged in
holoenzymes or complexes of specified size. Indeed, StochSim has been used to model clusters
of bacterial chemotactic receptors,[53] and CaMKII holoenzymes.[27]
An extension to StochSim has been presented by Colvin et al.[12] Their particle-based simulator
DYNSTOC uses a StochSim-like algorithm to simulate models specified in the BioNetGen language
(BNGL),[4] which improves the handling of molecules within macromolecular complexes.[12]
Another particle-based stochastic simulator that can read BNGL input files is RuleMonkey.[13] Its
simulation algorithm[9]differs from the algorithms underlying both StochSim and DYNSTOC in that the
simulation time step is variable.
The Network-Free Stochastic Simulator (NFSim) differs from those described above by allowing for
the definition of reaction rates as arbitrary mathematical or conditional expressions and thereby
facilitates selective coarse-graining of models.[14]RuleMonkey and NFsim implement distinct but
related simulation algorithms. A detailed review and comparison of both tools is given by Yang and
Hlavacek.[54]
It is easy to imagine a biological system where some components are complex multi-state
molecules, whereas others have few possible states (or even just one) and exist in large numbers. A
hybrid approach has been proposed to model such systems: Within the Hybrid Particle/Population
(HPP) framework, the user can specify a rule-based model, but can designate some species to be
treated as populations (rather than particles) in the subsequent simulation. [10] This method combines
the computational advantages of particle-based modeling for multi-state systems with relatively low
molecule numbers and of population-based modeling for systems with high molecule numbers and a
small number of possible states. Specification of HPP models is supported by BioNetGen, [4] and
simulations can be performed with NFSim.[14]

Spatial particle-based methods[edit]

Figure 3: Screenshot from an MCell simulation of calcium signaling within the spine. Although other types of
calcium-regulated molecules were included in the simulations, only CaMKII molecules are visualized. They are
shown in red when bound to calmodulin and in black when unbound. The simulation compartment is a
reconstruction of a dendritic spineas presented by Kinney et al. (J Comp Neurol. 2013).[55] The area of
thepostsynaptic density is shown in red, the spine head and neck in gray, and the parent dendrite in yellow. The
figure was generated by visualizing the simulation results in Blender.

Spatial particle-based methods differ from the methods described above by their explicit
representation of space.
One example of a particle-based simulator that allows for a representation of cellular compartments
is SRSim.[16][17] SRSim is integrated in the LAMMPS molecular dynamics simulator [56][57] and allows the
user to specify the model in BNGL.[4] SRSim allows users to specify the geometry of the particles in
the simulation, as well as interaction sites. It is therefore especially good at simulating the assembly
and structure of complex biomolecular complexes, as evidenced by a recent model of the
inner kinetochore.[58]
MCell[18][19][20][59] allows individual molecules to be traced in arbitrarily complex geometric environments
which are defined by the user. This allows for simulations of biomolecules in realistic reconstructions
of living cells, including cells with complex geometries like those of neurons. As an illustration, Figure
3 shows a screenshot from a simulation of calcium-regulated proteins. The reaction compartment is
a reconstruction of a dendritic spine.[55] Visualizations are supported by a specialized plug-in
("CellBlender") for the open source program Blender.[60]
MCell uses an ad-hoc formalism within MCell itself to specify a multi-state model: In MCell, it is
possible to assign "slots" to any molecular species. Each slot stands for a particular modification,
and any number of slots can be assigned to a molecule. Each slot can be occupied by a particular
state. The states are not necessarily binary. For instance, a slot describing binding of a
particular ligand to a protein of interest could take the states "unbound", "partially bound", and "fully
bound".
The slot-and-state syntax in MCell can also be used to model multimeric proteins or macromolecular
complexes. When used in this way, a slot is a placeholder for a subunit or a molecular component of
a complex, and the state of the slot will indicate whether a specific protein component is absent or
present in the complex. A way to think about this is that MCell macromolecules can have

several dimensions: A "state dimension" and one or more "spatial dimensions". The "state
dimension" is used to describe the multiple possible states making up a multi-state protein, while the
spatial dimension(s) describe topological relationships between neighboring subunits or members of
a macromolecular complex. One drawback of this method for representing protein complexes,
compared to Meredys, is that MCell does not allow for the diffusion of complexes, and hence, of
multi-state molecules. This can in some cases be circumvented by adjusting the diffusion constants
of ligands that interact with the complex, by using checkpointing functions or by combining
simulations at different levels.

Examples of multi-state models in biology[edit]

A (by no means exhaustive) selection of models of biological systems involving multi-state molecules
and using some of the tools discussed here is give in the table below.

Examples of multi-state models of biological systems

Biological system

Specification

Computa
tion

Refere
nce

Bacterial chemotaxis signalling

pathway

StochSim

StochSim

[61]

CaMKII regulation

StochSim

StochSim

[27]

ERBB receptor signalling

BioNetGen

NFSim

[29]

Eukaryotic synthetic gene

circuits

BioNetGen, PROMOT[62]

COPASI[63]

[30]

RNA signaling

Kappa

KaSim

[64]

Cooperativity of allosteric
proteins

Allosteric Network Compiler

(ANC)

MATLAB

[6]

Chemosensing in Dictyostelium

Simmune

Simmune

[44]

T-cell receptor activation

SSC

SSC

[65]

Human mitotic kinetochore

BioNetGen

SRSim

[66]

Cell cycle of fission yeast

ML-Rules

JAMES II[42]

[41]

What are biomolecules? 4

Different Types of Biomolecules
WHAT ARE BIOLMOLECULES
Biomolecules are those substance which are present exclusively in the living
organisms.
They are formed in the body to manage the needs of physiology and growth.
There are many biomolecules in nature and one can read them in detail
inbiochemistry.
Biochemistry describes their formation, physiological role and any deficiency
diseases.
The biomolecules are present in the body of humans, animals and plants.
Their primary formation from the basic elements seems to occur in plants.
Once formed, these molecules then pass on to animals through the food chain.
If you wish to directly go through list of biomolecules, you can refer to table at
the bottom of the article.

DIFFERENT TYPES OF BIOMOLECULES:

Biomolecules

1.
2.
3.

are

of

different

types

and

can

be

classified

as

Based on availability or source.

Based on their role or purpose in body.
Based on their chemistry.
Based on availability: Different types of biomolecules are available in different
set of organisms. Not all the bio-molecules of plants are available in animals and
vice-verse.
Hence based on the availability they can be divided as those available in

1.
2.
3.

plants
animals
Microbes.
Example: Lignin, chitin are biomolecules present only in plants in plant cell wall.
While the same cell wall in bacteria is made of gluco-polysacharrides glucopeptides are present in bacterial cell wall. While animals do not have a cell wall.
Hence there is difference of existence of biomolecules.
Besides these plants have alkaloids, glycosides, tannins, resins, gums etc. which
are specific to them.
In animals biomolecules like epinephrine, dopamine like substances are so
specific.

Based on purpose: Further these bio-molecules have different role and

purpose in body. So their existence in this manner is solely dependent on the
purpose.
Ex: Hemoglobin is a protein molecule formed in combination with iron (heme). It
is meant for oxygen supply in the body. It is available only in animals and
humans. But not available and also not needed for plants and microbes.
Though there are many biomolecules based on their role in body. Based on their
role in the body. There are 4 types of bio-molecules as.
1.
2.
3.
4.

Food sources.
Body elements
Primary metabolites
Secondary metabolites.
Food sources: These are the substances which act as food materials. They give
energy and nutrients to all the living beings on the earth.
Examples include: Carbohydrates, proteins, fats, vitamins.
Constitutional (Form Body) : These are the molecules which make up the
body structure. They also tend to control the body physiology.
Examples include: DNA, RNA, steroids, cholesterol etc. DNA forms the genes and
also mRNA, RNA from the body proteins. Steroids are part of many hormones.
Primary metabolites: These are the substances which act as intermediates in
the body metabolism and other reactions. They are formed from one or other
bio-molecules like food based or constitutional based.
Ex: UDP-Glucuronic acid, keto-glutaric acid etc.
Secondary metabolites: These are mostly end metabolic substances. They
are mostly excreted from the body.
Ex: Urea, uric acid, ketones etc.
Biomolecules are the natural substance present from birth to death of living
being. They are synthesized in the body by use of different elements from

nature. Substances like carbon-dioxide, ammonium, water and other inorganic

elements from soil contribute to the chemical formation of these molecules.

LIST OF BIOMOLECULES:
In a simple worksheet explaining characters, role and availability.
Biomolecul
e

Class

Characters

Presenc
e

Glucose

Carbohydrates.

Sweet in taste &

provides energy to
body

Animals
& plants

Sucrose
(sugar)

Sweet in taste &

provides energy to
body

Animals
& Plants

Starch

Breaks down to sugars

Animals
& plants

Cellulose

Breaks down to sugars

& eaten by animals

Plants

DNA

Nucleic Acid

Regulates Body
composition &
Physiology

Animals
& Plants

RNA

Nucleic Acid

Protein synthesis &

physiology

Animals
& Plants

Amino acids

Proteins

To make up proteins
and body building

Animals
& plants

Enzymes

Proteins

As catalysts to aid
reactions

Animals
& plants

Hormones

Amides, lipids, amines

Act as messengers to

Animals

Biomolecul
e

Class

Characters

Presenc
e

regulate physiology

& plants

Gums

Carbohydrates in
nature

Plants

Glycosides

Made of carbohydrate
+ Glycoside moiety

Metabolites but are

used in medicine

Plants

Tannins

Metabolites

Waste matter for plants

but used by humans

Plants

Cholesterol

Lipids

Forms cell membrane

Animals

Essential
oils

Hydrocarbons (volatile
oil which are gases at
high temperature.

As metabolites. To
attract insects for
pollination. Humans
use as perfumes.

Plants

Vitamins
A,B,C,D,E &
K

Vitamins

To aid in body
physiology

Animals
& Plants

This is not the end of the list but a brief categorization of biomolecules.
But of all those available, only 4 important biomolecules are studied widely.
These 4 major biomolecules include
1.
2.
3.
4.

Carbohydrates.
Proteins (amino-acids)
Fats
Nucleic acids (DNA, RNA, nucleotides).
These are studied so because of their role in health and diseases.

IMPORTANCE OF BIOMOLECULES:
Biomolecules are used for different purposes like food, medicine, cosmetics etc.
by humans. Below are few uses of them
1.
2.
3.
4.

Carbohydrates, proteins, fats are used as food stuffs in various forms.

Volatile oils or essential oils are used for perfumes.
Compounds like alkaloids, glycosides, tannins are used in medicine.
Tannins are also used to tan (toughen) the leather in industry.
These biomolecules are vital to the living beings. But they can be harmful and
toxic if misused or over stagnated in the body.

Biomolecules
Although there is vast diversity of living organisms. The chemical compositon and metabolic reactions of
the organisms appear to be similar. The composition of living tissues and non-living matter also appear to
be similar in qualitative analysis.Closer analysis reveals that the relative abundance of carbon, hydrogen
and oxygen is higher in living system.
All forms of life are composed of biomolecules only. Biomolecules are organic molecules especially
macromolecules like carbohydrates, proteins in living organisms. All living forms bacteria, algae, plant and
animals are made of similar macromolecules that are responsible for life. All the carbon compounds we
get from living tissues can be called biomolecules.

Biomolecules Definition
Back to Top

Biomolecules are molecules that occur naturally in living organisms. Biomolecules include
macromolecules like proteins, carbohydrates, lipids and nucleic acids. It also includes small molecules
like primary and secondary metabolites and natural products. Biomolecules consists mainly of carbon and

hydrogen with nitrogen, oxygen, sulphur, and phosphorus. Biomolecules are very large molecules of
many atoms, that are covalently bound together.

Classes of Biomolecules
Back to Top

There are four major classes of biomolecules:

Carbohydrates

Lipids

Proteins

Nucleic acids

Carbohydrates
Carbohydrates are good source of energy. Carbohydrates (polysaccharides) are long chains of
sugars. Monosaccharides are simple sugars that are composed of 3-7 carbon atoms. They have a free
aldehyde or ketone group, which acts as reducing agents and are known as reducing
sugars. Disaccharides are made of

two monosaccharides. The bonds shared between two

monosaccharides is the glycosidic bonds. Monosaccharides and disaccharides are sweet, crystalline and
water soluble substances.Polysaccharides are polymers of monosaccharides. They are unsweet, and
complex carbohydrates.They are insoluble in water and are not in crystalline form.

Example: glucose, fructose, sucrose, maltose, starch, cellulose etc.

Lipids
Lipids are composed of long hydrocarbon chains. Lipid molecules hold a large amount of energy and are
energy storage molecules. Lipids are generally esters of fatty acids and are building blocks of biological
membranes. Most of the lipids have a polar head and non-polar tail. Fatty acids can be unsaturated and
saturated fatty acids.
Lipids present in biological membranes are of three classes based on the type of hydrophilic head
present:

Glycolipids are lipids whose head contains oligosaccharides with 1-15 saccharide residues.

Phospholipids contain a positively charged head which are linked to the negatively charged
phosphate groups.

Sterols, whose head contain a steroid ring. Example steroid.

Example of lipids: oils, fats, phospholipids, glycolipids, etc.

Proteins
Proteins are heteropolymers of stings of amino acids. Amino acids are joined together by the peptide
bond which is formed in between the carboxyl group and amino group of successive amino acids.
Proteins are formed from 20 different amino acids, depending on the number of amino acids and
the sequence of amino acids.

There are four levels of protein structure:

Primary structure of Protein - Here protein exist as long chain of amino acids arranged in a
particular sequence. They are non-functional proteins.

Secondary structure of protein - The long chain of proteins are folded and arranged in a helix
shape, where the amino acids interact by the formation of hydrogen bonds. This structure is
called the pleated sheet. Example: silk fibres.

Tertiary structure of protein - Long polypeptide chains become more stabilizes by folding and
coiling, by the formation of ionic or hydrophobic bonds or disulphide bridges, this results in the
tertiary structure of protein.

Quaternary structure of protein - When a protein is an assembly of more than one polypeptide or
subunits of its own, this is said to be the quaternary structureof protein. Example: Haemoglobin,
insulin.

Nucleic Acids
Nucleic acids are organic compounds with heterocyclic rings. Nucleic acids are made of polymer of
nucleotides. Nucleotides consists of nitrogenous base, a pentose sugar and a phosphate group. A
nucleoside is made of nitrogenous base attached to a pentose sugar. The nitrogenous bases are adenine,
guanine, thyamine, cytosine and uracil. Polymerized nucleotides form DNA and RNA which are genetic
material.

Functions of Biomolecules
Back to Top

Carbohydrates provide the body with source of fuel and energy, it aids in proper functioning of our brain,
heart and nervous, digestive and immune system. Deficiency of carbohydrates in the diet causes fatigue,
poor mental function.
Each protein in the body has specific functions, some proteins provide structural support, help in body
movement, and also defense against germs and infections. Proteins can be antibodies, hormonal,
enzymes and contractile proteins.
Lipids, the primary purpose of lipids in body is energy storage. Structural membranes are composed of
lipids which forms a barrier and controls flow of material in and out of the cell. Lipid hormones, like sterols,
help in mediating communication between cells.
Nucleic Acids are the DNA and RNA, they carry genetic information in the cell. They also help in synthesis
of proteins, through the process of translation and transcription.

Structure of Biomolecules
Back to Top

Structure of biomolecule is intricate folded, three-dimensional structure that is formed by protein, RNA,
and DNA. The structure of these molecules are in different forms, primary, secondary, tertiary and
quaternary structure. The scaffold for this is provided by the hydrogen bonds within the molecule.

Primary structure of a biomolecule is the exact specification of its atomic composition and and the
chemical bonds connecting the atoms.

Secondary structure of the biomolecule is the three-dimensional form of biopolymers, secondary

structure is defined by the hydrogen bonds of the biomolecules.

Tertiary structure of the biomolecule is the three-dimensional structure,defined by its atomic

coordinates, by the formation of hydrogen, ionic or sulphide bonds.

Quaternary structure is the arrangement of multiple folds of complex, in a mutli-subunit complex.

Biomolecules - Definition, Types, Structure, Properties and Its

applications

Definition of Biomolecule:
An organic compound normally present as an essential component of living organism.

Characteristics of Biomolecules:
1) Most of them are organic compounds.
2) They have specific shapes and dimensions.
3) Functional group determines their chemical properties.
4) Many of them arc asymmetric.
5) Macromolecules are large molecules and are constructed from small building block
molecules.
6) Building block molecules have simple structure.
7) Biomolecules first gorse by chemical evolution.

Important Biomolecules of life:

1) Water: Being the universal solvent and major constituents (60%) of any living body
without which life is impossible. It acts as a media for the physiological and biochemical
reactions in the body itself. Maintain the body in the required turgid condition.
2) Carbohydrates: It is very important for source of energy for any physical body function.
3) Proteins: These are very important from body maintenance point of view,helps in tissue,
cell formation.
4) Lipids: These are very important from energy source as well as human nutrition point of
view.
5) Nucleic Acids: Nucleic acids are very important as DNA carries the hereditary
information and RNA helps in protein formation for the body.
6) Enzymes: Enzymes are simple or combined proteins acting as specific catalysts and
activates the various biochemical and metabolic processes within the body.

Table: Fundamental Biological Molecules (Biomolecules):

Sr. No.

Small Molecule

Atomic Constituents

Derived Macro - Molecule

Amino Acid

C, H, O, N (S)

Proteins

Sugars

C, H, O

Starch, Glycogen

Fatty Acids

C, H, O

Fats, Oils

Purines and
Pyrimidine

C, H, O, N

Nucleic Acids

Nucleotide

C, H, O, N, P

Nucleic Acids (DNA and RNA)